Optical Instruments and Systems for Forensic DNA Quantitation

ABSTRACT

Described herein are instruments for excitation and detection of fluorophores in a plurality of functional regions in a biochip, using an excitation source and a steering element that directs a beam from the excitation source to a plurality of functional regions in the biochip, wherein the excitation source excites the fluorophores in the plurality of functional regions generating a signal that is detected such that said signal from at least one of the plurality of functional regions allows for nucleic acid quantification. Also described are systems for quantification and separation and detection using optical devices adapted for preliminary, simultaneous or sequential quantitation of nucleic acid in separate detection positions, and for the excitation and detection of multiple samples to steer both the excitation and detection beam paths to separately image each lane of a biochip.

RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional PatentApplication Ser. No. 61/268,770, filed Jun. 15, 2009, entitled “ImprovedMethods for Forensic DNA Quantitation,” by Selden et al., which isincorporated herein by reference.

GOVERNMENT FUNDING

The U.S. Government has a paid-up license in this invention and theright in limited circumstances to require the patent owner to licenseothers on reasonable terms as provided for by the terms of (Grant No.NIJ 2008-DN-BX-K009) awarded by the National Institutes of Justice,Office of Justice Programs, US Department of Justice.

FIELD OF INVENTION

Described herein are inventive methods and devices for nucleic acidquantification and, in particular, to microfluidic methods and devicesfor nucleic acid quantification.

BACKGROUND

Nucleic acid quantification is a critical or desirable step in a widevariety of assays and applications. For example, nucleic acidquantification is an important step in human forensic identification.For example, short tandem repeat (STR) analysis of DNA is often based ona multiplexed PCR assay, and such assays are generally most reliablewithin a narrowly defined range of sample DNA concentration. If toolittle sample DNA is used in the assay, artifacts including allele peakheight imbalance and allele drop-out can occur. If too much sample DNAis used, artifacts including increased stutter, non-specific bandcreation, incomplete non-template addition, and pull-up peaks resultingfrom incomplete color separation can occur. These artifacts can lead todifficulties in interpretation of an STR profile but can be mitigated byusing an appropriate amount of sample DNA. In another example, forensiccasework samples have the potential to be contaminated with non-humanmammalian, bacterial, or fungal DNA which, when present, contributes tothe total DNA in the sample. Accordingly, for evaluation of crime scenesamples, the DNA Advisory Board to the FBI recommends the use ofhuman-specific quantification rather than total DNA quantification,which can ensure that an appropriate amount of human DNA is subjected toamplification even if bacterial, fungal, or other non-human DNA ispresent is the sample.

SUMMARY OF THE INVENTION

Described herein are inventive methods and devices for nucleic acidquantification and, in particular, to microfluidic methods and devicesfor nucleic acid quantification.

In one aspect, a method for quantifying a target nucleic acid in asample fluid containing or suspected of containing the target nucleicacid is provided. The method comprises combining in a microfluidicchannel the sample fluid and a binding agent comprising a signalingmoiety, wherein the binding agent becomes immobilized with respect tothe target nucleic acid, to form a test fluid, locating the test fluidin a detector region in the microfluidic channel, detecting thesignaling moiety, and quantifying the target nucleic acid in the samplefluid within 1 hour of combining the sample fluid and the binding agent.

In another aspect, a method for quantifying a target nucleic acid in asample fluid containing or suspected of containing the target nucleicacid is provided. The method comprises combining in a microfluidicchannel the sample fluid and a binding agent comprising a signalingmoiety, wherein the binding agent becomes immobilized with respect tothe target nucleic acid, to form a test fluid, locating the test fluidin a detector region in the microfluidic channel, detecting thesignaling moiety, and quantifying the target nucleic acid in the samplefluid, wherein the target nucleic acid has a concentration less than 1nanograms per microliter or is present in a total amount in the samplefluid of less than 1 nanogram.

In still another aspect, a method for quantifying a target nucleic acidin a forensic sample fluid containing or suspected of containing thetarget nucleic acid is provided. The method comprises combining in amicrofluidic channel the forensic sample fluid and a probe fluidcontaining a binding agent comprising a signaling moiety, wherein thetarget nucleic acid in the forensic sample fluid has not been amplified,locating the combined fluids in a detector region in the microfluidicchannel, detecting the signaling moiety, and quantifying the targetnucleic acid in the sample fluid.

In yet another aspect, a method for quantifying a target nucleic acid ina sample fluid containing or suspected of containing the target nucleicacid and also containing a contaminating non-human nucleic acid isprovided. The method comprises combining in a microfluidic channel thesample fluid and a probe fluid containing a binding agent comprising asignaling moiety, wherein the target nucleic acid in the sample fluidhas not been amplified, locating the combined fluid in a detector regionin the microfluidic channel, detecting the signaling moiety, andquantifying the target nucleic acid in the sample fluid.

In still another aspect, a method for quantifying of a target nucleicacid in a sample fluid containing or suspected of containing the targetnucleic acid is provided. The method comprises providing a microfluidicdevice coupled to an electronic device comprising a detector comprisingan integrated laser, combining in a microfluidic channel of themicrofluidic device the sample fluid and a binding agent comprising asignaling moiety, wherein the binding agent becomes immobilized withrespect to the target nucleic acid, locating the combined fluid in adetector region in the microfluidic channel positioned in operativeproximity to the detector of the electronic device, irradiating thesignaling moiety using the integrated laser, and quantifying the targetnucleic acid in the sample fluid.

In yet another aspect, a method for manipulating a target nucleic acidin a sample fluid containing the target nucleic acid is provided. Themethod comprises providing a microfluidic device comprising a pluralityof microfluidic channels and active areas for sample manipulationcoupled to an electronic device comprising a detector, combining in amicrofluidic channel of the microfluidic device the sample fluid and abinding agent comprising a signaling moiety, wherein the binding agentbecomes immobilized with respect to the target nucleic acid, locatingthe combined fluid in a detector region in the microfluidic channelpositioned in operative proximity to the detector of the electronicdevice, quantifying the target nucleic acid in the sample fluid, anddirecting a selected quantity of the sample fluid to an active area ofthe biochip, wherein said selected quantity is determined, at least inpart, based on the results of the quantifying step.

In still another aspect, a method for preparing a sample comprising atarget nucleic acid for amplification of the target nucleic acid isprovided. The method comprises providing a microfluidic devicecomprising at least one microfluidic channel and active areas for samplemanipulation, at least one of said areas configured to purify nucleicacid from a sample, obtaining the sample by a collection method yieldingan unknown variable quantity of target nucleic acid, inserting thesample into the microfluidic channel of the microfluidic device,purifying the target nucleic acid in the sample with the area of themicrofluidic device configured to purify nucleic acid from a sample toproduce a reproducible quantity of purified target nucleic acid, andamplifying, without quantifying the purified target nucleic acid, saidreproducible quantity of purified target nucleic acid.

In yet another aspect, a method for quantifying a target nucleic acid ina forensic sample fluid containing or suspected of containing the targetnucleic acid is provided. The method comprises combining in amicrofluidic channel the forensic sample fluid and a probe fluidcontaining a molecular beacon probe comprising a signaling moiety andhaving unique hybridization specificity for the target nucleic acid,wherein the target nucleic acid in the forensic sample fluid has notbeen amplified, locating the combined fluids in a detector region in themicrofluidic channel, detecting the signaling moiety, and quantifyingthe target nucleic acid in the sample fluid.

In still another aspect, an instrument for excitation and detection offluorophores in a plurality of functional regions in a biochip isprovided. The instrument comprises an excitation source and a steeringelement that directs a beam from an excitation source to a plurality offunctional regions in the biochip, wherein the excitation source excitesthe fluorophores in the plurality of functional regions generating asignal that is detected such that said signal from at least one of theplurality of functional regions allows nucleic acid quantification.

Other advantages and novel features of the present invention will becomeapparent from the following detailed description of various non-limitingembodiments of the invention when considered in conjunction with theaccompanying figures. Unless otherwise noted, all references citedherein are incorporated by reference in their entirety.

In cases where the present specification and a document incorporated byreference include conflicting and/or inconsistent disclosure, thepresent specification shall control.

BRIEF DESCRIPTION OF THE DRAWINGS

Non-limiting embodiments of the present invention will be described byway of example with reference to the accompanying figures, which areschematic and are not intended to be drawn to scale. In the figures,each identical or nearly identical component illustrated is typicallyrepresented by a single numeral. For purposes of clarity, not everycomponent is labeled in every figure, nor is every component of eachembodiment of the invention shown where illustration is not necessary toallow those of ordinary skill in the art to understand the invention. Inthe figures:

FIG. 1 shows a flowchart depicting various steps of target nucleic acidanalysis, according to an embodiment;

FIG. 2 shows an illustration of an exemplary integrated biochip foranalyzing four individual samples, according to an embodiment;

FIG. 3 shows a schematic of an optical train of a device configured toexcite and interrogate interrogation chambers of a quantification moduleas described in Example 10, according to an embodiment;

FIG. 4 shows a schematic of an optical train of a device configured toexcite and detect from the detection window of a separation anddetection module as described in Example 10, according to an embodiment;

FIG. 5 shows a schematic of an alternative optical train configured toexcite and interrogate the interrogation chambers of the quantificationmodule as described in Example 10, according to an embodiment;

FIG. 6 shows a schematic of an alternative optical train configured toexcite and detect from the detection window of the separation anddetection module as described in Example 10, according to an embodiment;

FIG. 7 shows a schematic of an alternative optical train configured toexcite and detect from the detection window of a separation anddetection module and interrogate the interrogation chambers of aquantification module as described in Example 10, according to anembodiment;

FIG. 8 shows an illustration of an exemplary excitation and detectionsystem, according to an embodiment;

FIG. 9 shows an illustration of another exemplary excitation anddetection system, according to an embodiment;

FIG. 10 shows a photograph of a biochip, according to an embodiment;

FIG. 11 shows a photograph of a thermal cycler comprising a chipcompression element and thermal control element (100), biochip (101),and thermosensor (102), according to an embodiment;

FIG. 12 shows a photograph of a view from above of a thermal cyclercomprising a TCE (1100), biochip (1101), thermosensor (1102),thermoelectric cooler (1103), heat sink (1104), and heat sinkthermosensor (1105), where the chip compression element has been removedfor clarity, according to an embodiment;

FIG. 13 shows a plot of input DNA (ng) versus baseline subtractedfluorescence signal (RFU) for a 28-cycle TH01 PCR-Picogreen reaction,according to an embodiment;

FIG. 14 shows a raw data plot of the output fluorescence signal fromTH01 PCR laser detection—peak intensities from left to right correspondto 0 ng, 0.4 ng, 1 ng, 4 ng, 10 ng, 20 ng and 40 ng input template DNA,according to an embodiment;

FIG. 15 shows a plot of input DNA (ng) versus baseline subtractedfluorescence signal (RFU) for a 15-cycle Alu PCR-Picogreen reaction,according to an embodiment;

FIG. 16 shows a raw data plot of the output fluorescence signal from AluPCR laser detection, according to an embodiment—peak intensities fromleft to right correspond to 0 ng, 0.4 ng, 1 ng, 4 ng, 10 ng, 20 ng and40 ng input template DNA;

FIG. 17 shows a plot of input DNA (ng) versus baseline subtractedfluorescence signal (RFU) for the 10-cycle Alu PCR reaction showingrepeatability of measurements, according to an embodiment—error barsrepresent 1 standard deviation;

FIG. 18 shows a plot of input DNA (ng) versus baseline subtractedfluorescence signal (RFU) for a 7-cycle Alu PCR-SYBR Green assay,according to an embodiment;

FIG. 19 shows a plot of baseline subtracted fluorescence signal (RFU)versus genomic DNA target concentration actually detected (pg) usingmolecular beacon probe 1 as described in Example 5, according to anembodiment;

FIG. 20 shows a plot of baseline subtracted fluorescence signal (RFU)versus genomic DNA target concentration actually detected (pg) usingmolecular beacon probe 2 as described in Example 5, according to anembodiment;

FIG. 21 shows a plot of baseline subtracted fluorescence signal (RFU)versus genomic DNA target concentration actually detected (pg) using1-minute hybridization with molecular beacon probe 2 as described inExample 6, according to an embodiment;

FIG. 22 demonstrates DNA binding “cut-off” as a function of the numberof purification filter layers as described in Example 9, according to anembodiment;

FIG. 23 demonstrates DNA binding performance of a 1 mm diameter filterover a range of input DNA as described in Example 9, according to anembodiment;

FIG. 24 shows a plot of signal strength as photomultiplier tube (PMT)gains are swept across the operation range as discussed in Example 10,according to an embodiment;

FIG. 25 shows a plot of signal-to-noise ratios as the PMT gains areswept across the operation range as discussed in Example 10, accordingto an embodiment;

FIG. 26 shows a plot of signal strength as a function of laser power asdiscussed in Example 10, according to an embodiment; and

FIG. 27 shows the photobleaching phenomenon with excitation level asdiscussed in Example 10, according to an embodiment.

BRIEF DESCRIPTION OF THE SEQUENCES

SEQ ID NO: 1 is TH01 Forward Primer having the sequence 5′-AGG GTA TCTGGG CTC TGG-3′;

SEQ ID NO: 2 is TH01 Reverse Primer having the sequence 5′-GCC TGA AAAGCT CCC GAT TAT-3′;

SEQ ID NO: 3 is Alu Forward Primer having the sequence 5′-GTC AGG AGATCG AGA CCA TCC C-3′;

SEQ ID NO: 4 is Alu Reverse Primer having the sequence 5′-TCC TGC CTCAGC CTC CCA AG-3′;

SEQ ID NO: 5 is PV 92 Probe 1 having the sequence 5′-GCC CGA TTT TGC GACTTT GGA GGG C-3′; and

SEQ ID NO: 6 is Alu Probe 2 having the sequence 5′-CGC CTC AAA GTG CTGGGA TTA CAG GCG-3′.

DETAILED DESCRIPTION

Described herein are inventive methods and devices for nucleic acidquantification and, in certain embodiments, to microfluidic methods anddevices for nucleic acid quantification. In one aspect, embodiments aregenerally related to methods of quantifying a target nucleic acid, suchas native (i.e. non-synthetic) nucleic acid without the need for prioramplification. The methods involve, in some embodiments, allowing abinding agent to become immobilized with respect to the target nucleicacid. In some cases, the binding agent comprises a signaling moiety thatcan be used to quantify the amount of target nucleic acid. In certainembodiments, the quantification can be carried out rapidly. For example,in certain embodiments, the quantification can be completed in 1 hour orless. In certain embodiments, samples containing a low amount of targetnucleic acid can be quantified, in certain embodiments using aflow-through microfluidic assay. For instance, in some cases, samplescontaining less than 1 nanogram may be quantified. In certainembodiments, the target nucleic acid may be quantified in the presenceof, non-target nucleic acids. Also provided are devices, biochips, andkits for performing methods of the inventions, or the like.

In some embodiments, the methods described herein may be particularlyuseful in forensic nucleic acid analysis. However, one of ordinary skillin the art would understand that the methods are not limited to forensicanalysis and can be used to analyze any suitable sample containing orsuspected of containing a target nucleic acid. In some embodiments,clinical and environmental samples may be analyzed. Certain embodimentsof the methods described herein may provide advantages over the priorart including one or more of, and not limited to, simplifiedquantification of nucleic acids, facile integration with microfluidicsystems, reduced reagent usage (i.e., in the amount of reagent usedand/or the number of reagents used), avoidance of reagents that canrequire special handling and/or storage such as enzymes, dNTPs, and PCRbuffers, speed of quantification, sensitivity of quantification,specificity of quantification, and improved ability to provideautomation. Also advantageously, the certain embodiments of the methodsdescribed herein can be used to analyze a target nucleic acid in asample despite its containing one or more PCR inhibitors, which can bepresent, for example, in clinical samples, environmental samples,forensic samples, and the like.

In some embodiments, the methods comprise combining a binding agentcomprising a signaling moiety with a sample suspected of containing anucleic acid strand containing a target sequence (i.e., a target nucleicacid) and determining whether or not there is a change in the signalingmoiety's measurable characteristic as compared to that characteristicunder essentially the same conditions in the absence of the targetnucleic acid. In some embodiments, it may be desirable to run a controlcontaining no target and to compare the response of the sample to theresponse of the control. In some cases, the level of signal may bemeasured for quantitative determinations. In certain such embodiments,the level of signal determined with a test sample may be compared with acalibration standard prepared using calibration samples containing knownconcentrations of nucleic acid strands containing the target sequence.In some embodiments, a change may simply be detected for the purpose ofconfirming the presence or absence of the target nucleic acid. Inembodiments where a control is used, the difference in signal changebetween the sample and the control may be calculated.

In some embodiments, multiple nucleic acid samples can beanalyzed/quantified essentially simultaneously. As discussed in moredetail below, multiple nucleic acid samples may be analyzed in parallelwith a microfluidic system comprising a microfluidic biochip,accompanying instrumentation, and software. In some embodiments, using amicrofluidic system allows multiple samples to be processed using anessentially identical set of manipulations for each sample (or subset ofsamples) using a tailored set of manipulations. Furthermore, in somecases, a plurality of independent sample treatments and/or analyses canbe performed in integrated fashion on a given sample. For example, aforensic sample may be analyzed by serially isolating DNA (i.e., thetarget nucleic acid), quantifying the isolated DNA, automaticallymetering a volume of DNA solution based on the quantification result,and then performing one or more of short tandem repeat (STR) analysis,single-nucleotide polymorphism (SNP) analysis, and mitochondrialsequencing on the isolated DNA. Similarly, a clinical sample may beanalyzed by purifying the target nucleic acid, quantifying the targetnucleic acid, automatically metering a volume of the nucleic solutionbased on the quantification result, and performing PCR,reverse-transcription PCR, and/or DNA sequencing on the target nucleicacid. In some embodiments, a sample may be interrogated for a one ormore pathogens, cellular processes, physiologic processes, drugs, andtoxins essentially simultaneously on a biochip. In some embodiments,sample analysis may be done automatically by a system.

FIG. 1 provides a flow chart depicting the various steps of targetnucleic acid analysis according to certain embodiments. In someembodiments, target nucleic acid analysis begins with step 100 whichinvolves obtaining a sample. In certain embodiments, the sample maycomprise a forensic sample, such as a crime scene or evidence sample. Insome cases, the target nucleic acid may be extracted from the sample asin step 110, for example, to prepare the sample for the mixing of thetarget nucleic acid with a binding agent comprising a signaling moietyof step 120. The steps may involve immobilizing the binding agent withrespect to the target nucleic acid as in step 130 and detecting thesignaling moiety as in step 140. The target nucleic acid may then bequantified as in step 150 using techniques described in more detailbelow. It should be understood that some methods may not include all ofthese steps and/or may include additional steps not illustrated. Forexample, in some cases the target nucleic acid may not need to beextracted, thereby obviating step 110.

In some embodiments, a sample may be obtained as in step 100. A samplemay be obtained by any suitable method. For example, a buccal swab maybe obtained. Generally, a buccal swab uses a collection device, forexample, a small brush or cotton swab, to collect a sample of cells fromthe inside surface of the cheek. Alternatively, a small amount ofmouthwash (i.e., saline mouthwash) may be swished in the mouth tocollect the cells. In some embodiments, other methods may be used tocollect a sample of blood, saliva, semen, amniotic fluid, hair, skin, orother appropriate fluid and/or tissue. The wide range of samples alsoincludes vaginal swabs, cervical swabs, urethral swabs, rectal swabs,nasal swabs, nasopharyngeal swabs, wound swabs, biopsy specimens, marrowaspirates, and sputum aspirates. A sample, in some embodiments, may beobtained from personal items (e.g. toothbrush, razor), items touched byan individual (e.g. the rim of a drinking glass, a shirt collar, the rimof a cap, a doorknob, a window pane, or a table) stored samples (e.g.banked sperm or biopsy tissue), a corpse, a victim, a perpetrator, asuspect, a crime scene, a patient, or a relative (i.e., a bloodrelative). In some cases, the sample nucleic acids may be unpurified,partially purified, or purified. In some embodiments, the sample nucleicacids may be essentially free of contaminating target nucleic acid. Inother embodiments, the sample may contain a mixture of target nucleicacids and non-target nucleic acids (e.g. a human DNA sample for forensicanalysis may also contain canine DNA). For example, the sample may be anin vitro or an in vivo sample. Generally, a sample contains a targetnucleic acid or is suspected of containing a target nucleic acid. Itshould be understood that “sample” may refer to the target nucleic acid,a mixture (solid and/or liquid) containing the target nucleic acid, or amaterial (solid and/or liquid) suspected of containing the targetnucleic acid.

A sample may contain at least some target nucleic acid or may contain notarget nucleic acid. In some embodiments, the quantity of target nucleicacid in the sample may be dependent on the method used to obtain thesample (i.e., the collection method). In some embodiments, thecollection method may yield a quantity of target nucleic acid within arange of essentially 0 to 100 μg, within a range of 1 pg to 100 μg,within a range of 1 ng to 100 μg, within a range of 10 ng to 100 μg,within a range of 100 ng to 100 μg, within a range of 1 pg to 10 μg,within a range of 1 ng to 10 μg, within a range of 10 ng to 10 μg, orwithin a range of 100 ng to 10 μg. In some embodiments, the quantity oftarget nucleic acid collected by the collection method may differ from afirst sample to a second sample by at least a factor of 10, at least afactor of 100, at least a factor of 1000, or at least a factor of 10000.

A sample may contain one or more compositions other than the targetnucleic acid (if present). For example, a sample collection fluid may beused to collect, dilute, suspend, or dissolve, a sample. Generally, thesample collection fluid may be aqueous; however, the sample collectionfluid may also comprise an organic solvent instead of or in addition tothe aqueous solvent. In various other embodiments, the sample collectionfluid may contain one or more buffers, stabilizers, enzyme inhibitors(e.g., nuclease inhibitors), chelating agents, salts, or othercompositions. In another embodiment, following collection of the samplewith the sample collection fluid, the sample may be allowed to dry(e.g., forensic swab samples may be dried and processed at a latertime). In yet another embodiment, no sample collection fluid may beutilized (e.g., a dry swab may be used).

In some embodiments, the target nucleic acid (if present) may beextracted (e.g., purified) from the sample as in step 110. In somecases, the target nucleic acid may be extracted in a microfluidicbiochip. However, one of ordinary skill in the art would recognize thatthe target nucleic acid may also be extracted by any of a number ofextraction methods known in the art, many of which are commerciallyavailable. For example, a liquid-liquid extraction technique may beused, such as those involving phenol-chloroform solutions. In anotherexample, a liquid-solid extraction technique may be used, where a sampleis collected on a solid substrate and washed, generally with a pluralityof solutions, to isolate the target nucleic acid (see, for example, kitssold by Qiagen Corporation). Other examples of nucleic acid purificationmay be found, for example, in U.S. patent application Ser. No.12/699,564, entitled “Nucleic Acid Purification,” filed Feb. 3, 2010, bySelden et al., which is incorporated herein by reference.

In embodiments where the target nucleic acid is isolated from a cellularsample (i.e., a cell, a plurality of cells, a mixture of cells, one ormore cells within a tissue), the cell(s) may be broken open (e.g.,disrupted or lysed). In some embodiments, the membrane lipids of thecell may be disrupted using a detergent. In some cases, proteins may bebroken down by treating the sample with one or more proteases. In someinstances, proteins may be removed by precipitation, for example, withan acetate salt such as sodium acetate or ammonium acetate. In someembodiments, proteins may be removed using phenol-chloroform phaseseparation. In some embodiments, the target nucleic acid may beprecipitated, for example, using an alcohol such as ethanol orisopropanol. In some cases, guanidinium thiocyanate-phenol-chloroformmay be used, for example, to extract an RNA or DNA target nucleic acid.A partially purified or purified target nucleic acid can be solubilizedin any suitable solution (e.g. collection fluid), for example, deionizedwater or a buffer such as tris-EDTA (TE). Other techniques for purifyingDNA and/or RNA will be known to those skilled in the art.

As discussed above, any sample containing or suspected of containing atarget nucleic acid may be analyzed. The target nucleic acid may be anynucleic acid. For example, in some embodiments, the target nucleic acidmay be DNA, RNA or mixtures or copolymers thereof. In some embodiments,the target nucleic acid (and other types of nucleic acids, as aredescribed herein) may be genomic DNA, chromosomal DNA, extrachromosomalDNA, plasmid DNA, mitochondrial DNA, chloroplast DNA, cDNA, rRNA, mRNA,or fragments thereof. The target nucleic acid may be isolated fromnatural sources (i.e. native), recombinantly produced, or artificiallysynthesized. For example, the target nucleic acid may be isolated from ahuman cell, a bacterial cell, a fungal cell, a eukaryotic cell, aprokaryotic cell, or a virus. In some cases, the target nucleic acid maybe synthetic (i.e., a product generated by amplification [e.g. PCR,quantitative PCR, reverse transcription PCR], ligation, or a chemicalsynthesis). The target nucleic acid may be a nucleic acid that encodes abiological entity, such as a protein, an enzyme, an antibody, areceptor, a ribozyme, a ribosome, or the like, or a portion thereof. Asanother non-limiting example, the target nucleic acid may be aregulatory sequence or a non-coding sequence, for instance, a smallinterfering RNA, a microRNA, a small hairpin RNA, or the like. In someembodiments, the target may be a unique genomic sequence or a repetitivegenomic sequence. The target nucleic acid and/or the target sequence canbe any number of nucleotides in length, for example, on the order of 12,14, 16, 18, 20, 22, 25, 30, 35, 40, 45, 50, 60, 70, 80, 90, 100, 200,400, 800, 1600, 3200, 6400 or more nucleotides in length. A nucleic acidmay contain residues such as the naturally-occurring bases (e.g.,adenosine or “A,” thymidine or “T,” guanosine or “G,” cytidine or “C,”or uridine or “U”), or other residues, such as methylated residues. Thenucleic acid can be single-stranded in some cases to facilitatehybridization.

In some embodiments, a target nucleic acid can also be amplified usingnucleic acid amplification techniques, such as PCR (polymerase chainreaction) or the like. Various copies of the target nucleic acid can belabeled with a signaling entity (e.g. a fluorescent dye). The signalingentity may be included within the nucleic acid at any suitable location,for example, at a 5′ terminal site of the nucleic acid sequence, a 3′terminal site, or at an internal site within the nucleic acid.

In some embodiments, the sample may contain target nucleic acids frommore than once source. For example, the sample may contain a firsttarget nucleic acid and a second nucleic acid. In some cases, both thefirst target nucleic acid and the second nucleic acid may be from afirst human and a second human, respectively. In some embodiments, thefirst target nucleic acid may be from a human and the second targetnucleic acid may be from a non-human (e.g., a bacterium, a mouse, a dog,a cat, a reptile, a snake, an insect, a non-human primate, etc.). Insome cases, the sample may contain two, three, four, five, six, seven,eight, nine, ten, or more distinct types of nucleic acids, one, some, orall of which may be a target nucleic acid.

In some embodiments, the sample may be combined with a binding agent asin step 120 to form a test fluid. The test fluid may be any sample fluidcontaining a binding agent. As discussed in more detail below, thebinding agent is an entity capable of being specifically immobilizedwith respect to a target nucleic acid. As discussed above, in somecases, the sample may be a fluid (i.e., a sample fluid). In someembodiments, the binding agent may be contained in a fluid (hereinafter“a probe fluid”). In some embodiments, the sample fluid and/or probefluid may be aqueous and/or organic. In some cases, the sample fluidand/or probe fluid may contain one or more buffers, stabilizers, enzymeinhibitors (e.g., nuclease inhibitors), chelating agents, salts, orother compositions.

In some embodiments, the binding agent may be attached to themicrofluidic device. For example, in some instances, the binding agentmay be covalently attached to the wall of a microfluidic channel. Insome cases, the binding agent may be non-covalently attached to a wallor feature of a microfluidic channel. In some embodiments, the targetnucleic acid may be attached to the microfluidic device (i.e.,covalently or non-covalently). In some embodiments, a microfluidicchannel may have a region suitable for binding a binding agent and/or atarget nucleic acid. For example, the binding agent and/or targetnucleic acid may be flowed through a first region of a microfluidicchannel without substantially binding to a feature and bind to a featurein a second region of a microfluidic channel. In certain embodiments,neither the target nucleic acid nor the binding agent are or becomeattached to the wall of any microfluidic channel during the assay, butrather remain suspended in the test fluid.

In some instances, the sample fluid and the probe fluid may be combined.For example, the sample fluid and the probe fluid may be combined in amicrofluidic system (e.g., in a microfluidic channel or a mixingcompartment of a microfluidic channel containing system). The sample andthe binding agent may be mixed using any suitable technique. Forexample, the sample fluid and probe fluid may be mixed by vortexing orpipetting the combined samples. In some embodiments, the sample fluidand probe fluid can be mixed in a microfluidic system. One of ordinaryskill in the art will be aware of devices and channel configurations formixing fluids in a microfluidic system, non-limiting examples of whichare disclosed in International Patent Application Publication No.WO/2008/124104, entitled “Integrated Nucleic Acid Analysis,” filed Apr.4, 2008, by Tan et al., which is incorporated by reference herein.

The binding agent may be any entity capable of being immobilized withrespect to a target nucleic acid comprising a target sequence. In someembodiments, the binding agent may become immobilized with respect tothe target nucleic acid through non-covalent bonds. For example, thenon-covalent bonds may comprise one or more of hydrogen bonds, van derWaals interactions, hydrophobic interactions, etc. In some cases, thebinding agent may become immobilized with respect to the target nucleicacid through one or more covalent bonds.

In some embodiments, the binding agent may be capable of beingspecifically immobilized to a target sequence of a target nucleic acid(i.e., the binding agent may be a specific binding agent having uniquespecificity for the target nucleic acid). For example, the binding agentmay be preferentially immobilized (e.g. hybridized) to a first targetnucleic acid having a first sequence relative to a second target nucleicacid having a second sequence, the second sequence being different fromthe first sequence. In some cases, the binding agent may be capable ofbeing immobilized non-specifically to target nucleic acid. For example,the binding agent may intercalate into a target nucleic acidsubstantially independently of the target nucleic acid sequence. In someembodiments, the binding agent may be an intercalating dye, anintercalating fluorescent dye, or an intercalating fluorescent dyecapable of selectively intercalating with double stranded nucleic acids.

In some embodiments, the binding agent may be a nucleic acid, i.e., thebinding agent may be a nucleic acid probe. One of ordinary skill in theart would recognize that a nucleic acid probe may be designed to have asequence that can hybridize to a target nucleic acid having a sequencethat is at least partially complementary to the sequence of the nucleicacid probe under a given set of annealing conditions. One of ordinaryskill in the art would also recognize that the sequence homology betweenthe target nucleic acid and the nucleic acid probe need not be perfect.For example, in some embodiments, a target nucleic acid and nucleic acidprobe pair may have one or more mismatches.

In some embodiments, a binding agent (e.g., a nucleic acid probe) and atarget nucleic acid may be hybridized by heating a sample containing thebinding agent and target nucleic acid to a first temperature and thencooling the sample to a second temperature. In some cases, the firsttemperature may be held for a period of time before cooling to thesecond temperature. For instance, the first temperature may be held forless than 1 second, less than 5 seconds, less than 10 seconds, less than30 seconds, less than 1 minute, or less than 5 minutes. Of course,temperatures outside these ranges may be used as well. In someembodiments, the first temperature may be above the melting temperature(i.e. temperature at which hybridized complementary strands dissociate,T_(m)) of the hybridized binding agent and target nucleic acid. In someembodiments, the first temperature may be within 5° C. of the T_(m) ofthe hybridized binding agent and target nucleic acid. In someembodiments, the first temperature may be at least 30° C., at least 40°C., at least 50° C., at least 60° C., at least 70° C., at least 80° C.,at least 90° C., or at least 95° C. The second temperature may be atleast 5° C., at least 10° C., at least 20° C., at least 30° C., at least40° C., at least 50° C., at least 60° C., at least 70° C., at least 80°C., at least 90° C. lower than the first temperature. In someembodiments, the rate at which the temperature is cycled between thefirst temperature and the second temperature may be at least 1°C./second, 5° C./second, 10° C./second, 20° C./second, 30° C./second,50° C./second, 100° C./second, or 200° C./second. In certain cases,according to the invention, rapid thermal cycling provided by certainsystems and methods of the invention can enable, at least in part, theability to analyze, detect and/or quantify target nucleic acid morequickly than typical conventional methods. For example, in someembodiments, rapid thermal cycling may allow the concentration of atarget nucleic acid in a sample fluid to be determined within a shortperiod of time after combining the sample fluid and a binding agent.

As discussed above, the target nucleic acid may be recognized by (e.g.hybridize with) one or more binding agents. Nucleic acid binding agentscan be used in various embodiments to target certain sequences within atarget nucleic acid. Often, short portions of the target nucleic acidcan be associated with a nucleic acid probe, for instance, a sequence ofless than 50 residues, less than 30 residues, less than 20 residues,less than 15 residues, less than 10 residues, less than 9 residues, lessthan 8 residues, less than 7 residues, less than 6 residues, less than 5residues, and less than 4 residues. In some embodiments, a nucleic acidprobe may contain a relatively short sequence of nucleic acid residuesthat is able to recognize at least a portion of the target nucleic acid(i.e., the sequences are complementary, or at least substantiallycomplementary), and often has a similar length as the recognized portionof the target nucleic acid. For instance, the nucleic acid probe mayhave a sequence having a length of less than 10000 nucleotides, lessthan 1000 nucleotides, less than 500 nucleotides, less than 250nucleotides, less than 100 nucleotides, less than 75, 50, 40, 35, 30,25, 24, 22, 20, 18, 16, 14, or 12 nucleotides. The selection of thestructure, sequence, length, and annealing conditions for a nucleic acidprobe sequence are well known in the art. The nucleic acid probes may besynthesized using any suitable technique, e.g., solid phasephosphoramidite triester methods. Other methods will be known to thoseskilled in the art. Nucleic acid probes may also be obtainedcommercially, for example, from Integrated DNA Technologies, Inc.

The nucleic acid sequences within the nucleic acid probe may becontiguous, or the sequence may be noncontiguous. For instance, theremay be universal residues or gaps present within the probe sequence.Additionally, secondary structures such as hairpins, loops, etc. may bepresent in some cases, which may be used to create a noncontiguoussequence. As a non-limiting example, a nucleic acid probe may have afirst and second region that are at least substantially complementary toa contiguous sequence of the target nucleic acid and are separated by athird region that is not complementary to the contiguous sequence of thetarget nucleic acid. The nucleic acid probe may hybridize to the targetnucleic acid such that the third region forms a hairpin, therebyallowing the first and second regions to hybridize to the contiguoustarget nucleic acid sequence in a noncontiguous fashion.

In some cases, a nucleic acid probe may hybridize to a substantiallycomplementary sequence without creating an overhang (i.e., without atleast some of the residues within the nucleic acid probe extending pasta terminus of the target nucleic acid). Alternatively, in someinstances, a nucleic acid probe may hybridize to a target nucleic acidsuch that at least one residue of the nucleic acid probe extends beyonda terminus of the target nucleic acid.

A nucleic acid probe need not hybridize completely with a target nucleicacid. The hybridization of two nucleic acids and/or nucleic acid analogscan be affected by a variety of factors, and the strength ofhybridization of particular residues within a given duplex can bedifferent.

As used herein, a first sequence that is “substantially complementary”to a second sequence is one in which at least 75% of the first andsecond sequences are complementary (e.g., through Watson-Crickcomplementary pairing). For example, in a situation where a targetsequence is 24 bases in length, the probe sequences would be“substantially complementary” even if they have a maximum of 6 base pairmismatch. In some embodiments, the two sequences may be at least 80%,85%, 90%, or 100% complementary.

In certain embodiments, a nucleic acid probe may comprise at least oneresidue that can enhance residue stacking and/or backbonepre-organization. This can significantly increase the thermal stability(melting temperature) of the nucleic acid probe in some cases. Forexample, a nucleic acid probe may comprise at least one locked nucleicacid (LNA) residue. A locked nucleic acid residue is a nucleic acidanalog that has a chemical shape similar to a naturally occurringnucleic acid residue (e.g., being able to form 2 or 3 hydrogen bondswith a complementary residue), but is not free to rotate in as manydimensions as a naturally occurring nucleic acid residue. For instance,in some cases, a locked nucleic acid residue may contain a 2′-O, 4′-Cmethylene bridge, where the methylene bridge “locks” the ribose in the3′-endo structural conformation, which is often found in the certainform of DNA or RNA. In some cases, the locked ribose conformation maysignificantly increase the thermal stability of the nucleic acid probe.Other residues that can increase the thermal stability of a nucleic acidsequence will be apparent to those skilled in the art. For example,peptide nucleic acids may be used as nucleic acid probes in some cases.

In certain embodiments, the nucleic acid probe can contain a universalresidue, which may be able to engage in a residue-pairing relationshipwith more than one natural nucleotide, and in some cases, with all ofthe natural nucleotides. A universal base or universal residue (e.g.,“N”), as used herein, refers to a base that, when incorporated into apolymeric structure in the form of a nucleobase (e.g., a nucleotide or aPNA) does not significantly discriminate between bases on acomplementary polymeric structure having nucleobases. For example, auniversal base can hybridize to more than one nucleotide selected fromA, T, C, and G. Universal residues will be known to those or ordinaryskill in the art. Non-limiting examples of universal residues includedeoxyinosine, 3-nitropyrrole, 4-nitroindole, 6-nitroindole,5-nitroindole, 6-methyl-7-azaindole, pyrrollpyrizine, imidizopyridine,isocarbostyril, propynyl-7-azaindole, propynylisocarbostyril,allenyl-7-azaindole, 8-aza-7-deaza-2′-deoxyguanosine,8-aza-7-deaza-2′-deoxyadenosine, 2′-deoxycytidine, 2′-deoxyuridine,2′-deoxyadenosine, 2′-deoxyguanosine, 7-deaza-2′-deoxyinosine,2′-aza-2′-deoxyinosine, 3′-nitroazole, 4′-nitroindole, 5′-nitroindole,6′-nitroindole, 4-nitrobenzimidazole, nitroindazole (e.g.,5′-nitroindazole), 4-aminobenzimidazole, imidazo-4,5-dicarboxamide,3′-nitroimidazole, imidazole-4-carboxamide, 3-(4-nitroazol-1-yl)-1,2-propanediol, and 8-aza-7-deazaadenine. Other universal residues usefulfor the systems and methods described herein will be known to those ofskill in the art.

In some embodiments, the binding agent may comprise a signaling moiety.The signaling moiety may be any entity capable of generating a signal.In some embodiments, the signaling moiety is attached to the bindingagent (i.e., through one or more covalent or non-covalent bonds). Insome embodiments, the signaling moiety may not be attached to thebinding agent. For example, in some cases, the signaling moiety mayassociate with the binding agent during or after immobilization of thebinding agent with respect to the target nucleic acid. In some cases,the signaling moiety may associate with the target nucleic acid.

In some embodiments, the signaling moiety may comprise a fluorophore,fluorophore/quencher pair, chromophore, radiolabel, enzymatic substrate,colorimetric substrate, spin label, isotope such as a non-radioactiveisotope or an isotope detectable by mass spectrometry (e.g., anelectrophore mass label (EML)), ligand which can serve as a bindingpartner to a labeled antibody, enzyme, antibody which can serve as abinding partner for a labeled ligand, antigen, group having a specificreactivity, and/or electrochemically detectable moiety. In someembodiments, the signaling moiety may be a particle (e.g., a fluorescentparticle, quantum dot, etc.). One of ordinary skill in the art would beable to identify other suitable signaling moieties. In some cases, thesignaling moiety may generate a signal upon stimulation, for example,with light (e.g., in the case of a fluorophore or chromophore). In someinstances, the signaling moiety may spontaneous generate a signal, suchas in the case of a radiolabel. In certain embodiments, the ability ofthe signaling moiety to generate a detectable signal may be dependent onthe proximity of a first component and a second component of thesignaling moiety. It should be understood that the first component andsecond component may be connected through one or more bonds or may benot be connected (i.e., may be separable).

In some embodiments, the signaling moiety may comprise a fluorophore.Non-limiting examples of fluorophores include dyes that can besynthesized or obtained commercially (e.g. Operon Biotechnologies,Huntsville, Ala.). A large number of dyes (greater than 50) areavailable for application in fluorescence excitation applications. Thesedyes include those from the fluorescein, rhodamine AlexaFluor, Biodipy,Coumarin, and Cyanine dye families Specific examples of fluorophoresinclude, but are not limited to, FAM, TET, HEX, Cy3, TMR, ROX, Texasred, LC red 640, Cy5, and LC red 705. In some embodiments, dyes withemission maxima from 410 nm (e.g., Cascade Blue) to 775 run (e.g., AlexaFluor 750) are available and can be used. Of course, one of ordinaryskill in the art will recognize that dyes having emission maxima outsidethese ranges may be used as well. In some cases, dyes ranging between500 nm to 700 nm have the advantage of being in the visible spectrum andcan be detected using conventional photomultiplier tubes. In someembodiments, the broad range of available dyes allows selection of dyesets that have emission wavelengths that are spread across the detectionrange. Detection systems capable of distinguishing many dyes are knownin the art.

In some embodiments, the signaling moiety may be conjugated to thebinding agent. For example, a signaling moiety and nucleic acid probemay be conjugated, for example, by forming an ester bond between the 3′hydroxyl group of the nucleic acid and a linker attached to a signalingmoiety. The linker may be any suitable linker. For example, the linkermay be of sufficient length to allow a nucleic acid probe to hybridizeto a target nucleic acid. Other techniques will be known to those ofordinary skill in the art.

In some embodiments, a quencher can be used for labeling oligo sequencesto minimize background fluorescence or for use in fluorophore/quencherpairs, as described elsewhere herein. Quenchers are known to those ofordinary skill in the art. Non-limiting examples of quenchers includeDDQ-I, Dabcyl, Eclipse, Iowa Black FQ, BHQ-1, QSY-7, BHQ-2, DDQ-II, IowaBlack RQ, QSY-21, and BHQ-3. In some embodiments, a quencher may have anabsorption maximum within the range of 430 nm (e.g., DDQ-I) to 670 nm(e.g., BHQ-3).

In some embodiments, the binding agent comprising a signaling moiety maybe a molecular beacon, for instance, as discussed in U.S. Pat. No.5,925,517, entitled “Detectably Labeled Dual ConformationOligonucleotide Probes, Assays and Kits,” issued Jul. 20, 1999, by Tyagiet al, which is hereby incorporated by reference. The binding agent(e.g., molecular beacon) may have a target nucleic acid complementsequence flanked by members of an affinity pair, or arms, that, underassay conditions in the absence of target, interact with one another toform a stem duplex. Hybridization of the binding agent to itspreselected target sequence can produce a conformational change in thebinding agent, forcing the arms apart and eliminating the stem duplex.Embodiments of binding agents employ interactive labels, whereby thatconformational change can be detected. In some embodiments, the bindingagent may comprise at least a single-stranded nucleic acid sequence thatis substantially complementary to a desired target nucleic acid, hereinreferred to as a “target complement sequence;” 5′ and 3′ regionsflanking the target complement sequence that reversibly interact bymeans of either complementary nucleic acid sequences or by attachedmembers of another affinity pair; and a signaling moiety comprisinginteractive label moieties for generating a signal. In some embodiments,the binding agent includes substantially complementary nucleic acidsequences, or “arms,” that reversibly interact by hybridizing to oneanother under the conditions of detection when the target complementsequence is not bound to the target. In some embodiments, the bindingagent comprising a signaling moiety may be unimolecular, i.e., all theabove components may be in one molecule. In instances where the bindingagent is bimolecular, half, or roughly half, of the target complementsequence, one member of the affinity pair and one member of the labelpair may be in each molecule.

The signal generating label moieties of the signaling moiety may haveinteractive label “pairs” matched such that at least one label moietycan alter at least one physically measurable characteristic of anotherlabel moiety when in close proximity but not when sufficientlyseparated. In some embodiments, the label moieties may be conjugated tothe probe such that the proximity of the label moieties to each othercan be regulated by the status of the interaction of the affinity pair.In the absence of target, the label moieties may be held in closeproximity to each other by the linking interaction of the affinity pair.This conformation may be referred to as the “closed” state. When thedetectable signal of the signaling moiety is not generated in the closedstate, which is generally the case with most embodiments, the closedstate can be considered to be in the “off” state.

In instances where the target complement sequence hybridizes to itstarget, a conformational change may occur in the binding agent,separating the affinity pair and, consequently, the label moieties ofinteractive labels. This conformation may be referred to as the “open”state, which in most embodiments can be considered the “on” state.Without wishing to be bound by any theory, separation is believed to bedriven by the thermodynamics of the formation of the target complementsequence-target sequence helix. Formation of the target complementsequence-target sequence helix, whether complete or nicked, overcomesthe attraction of the affinity pair under assay conditions. A signal isgenerated because the separation of the affinity pair alters theinteraction of the label moieties and a difference in at least onecharacteristic of at least one label moiety conjugated to the bindingagent may be measured.

In some embodiments, a binding agent having interactive labels has ameasurable characteristic (e.g., a detectable signal) that differsdepending on whether the binding agent is open or closed. Generally, themeasurable characteristic is a function of the interaction of the labelmoieties and the degree of interaction between those moieties thatvaries as a function of their separation.

As discussed above, a binding agent may have a closed conformation andan open conformation. In the closed conformation, the label moieties maybe “proximate” to one another, that is, they may be sufficiently closeto interact so that the signal differs (e.g., in detectable amount,quality, level, etc.) from the open conformation, when they may notinteract. In some cases, it may be desirable that the difference be aslarge as possible. In some cases, it may be desirable that in the “off”state the measurable characteristic be a signal as close as possible tozero.

In some embodiments, the measurable characteristic (e.g., detectablesignal) may be a characteristic light signal that results fromstimulating at least one member of a fluorescence resonance energytransfer (FRET) pair. In some cases, the signal may be a color changethat results, for example, from the action of an enzyme/suppressor pairor an enzyme/cofactor pair on a substrate to form a detectable product.In some embodiments, the binding agent comprising a signaling moiety mayhave a characteristic signal whose level depends on whether the labelmoieties are proximate due to the binding agent being in the closedposition or are separated due to the binding agent being in the openposition.

In some embodiments, the choice of label moieties can dictate in whichstate a signal is generated. In some cases, the choice of label moietiescan dictate that different signals are generated in each state. In someembodiments, the interactive label moieties may be afluorophore/quencher pair. In some instances, the interactive labelmoieties may be covalently conjugated to the binding agent. In somecases, the interactive label moieties may be conjugated to arm portionsof the binding agent that are not complementary to the target nucleicacid. In certain instances, the signaling moiety can generate a positivefluorescent signal of a particular wavelength when the binding agent isbound to the target nucleic acid in the open state and stimulated withan appropriate light source.

As discussed above, the binding agent may be immobilized with respect tothe target nucleic acid as in step 130. The immobilization may becarried out using any suitable technique. For example, in someembodiments, the binding agent and the target nucleic acid may be heatedand then cooled over a period of time to facilitate immobilization(e.g., hybridization). In some embodiments, immobilization may occurwithout the need for a heating-cooling cycle. In some cases, a chemicalreaction may be occur that immobilizes the binding agent with respect tothe target nucleic acid. For example, a crosslinking reagent may be usedto bond the binding agent and the target nucleic acid covalently.

The immobilization may, according to certain embodiments of theinvention, be effected in a short period of time. In some embodiments,the overall time for quantifying a target nucleic acid can besignificantly reduced because of the rapid immobilization time. Forexample, in certain embodiments, a microfluidic system including a rapidthermal cycler may be used to allow the binding agent and the targetnucleic acid to achieve the desired target temperatures such that thereaction can be completed in less than 1 hour, in certain embodimentsless than 30 minutes, in certain embodiments less than 20 minutes, incertain embodiments less than 10 minutes, in certain embodiments lessthan 5 minutes, in certain embodiments less than 1 minute, in certainembodiments less than 30 seconds, in certain embodiments less than 10seconds, in certain embodiments less than 5 seconds, in certainembodiments less than 1 second, and in certain embodiments substantiallyinstantaneously. Devices and methods for thermal cycling have beendescribed, for example, in U.S. Patent Application Publication No.2009/0023603, entitled “Methods for Rapid Multiplexed Amplification ofTarget Nucleic Acids,” filed Apr. 4, 2008, by Selden et al., which isincorporated herein by reference.

In some embodiments, the signaling moiety may generate a detectablesignal (i.e., measurable characteristic). In some embodiments, thedetectable signal may be a light signal (e.g., fluorescence orchemiluminescence). As discussed above, in some embodiments, thedetectable signal may be a characteristic light signal that results fromstimulating at least one member of a fluorescence resonance energytransfer (FRET) pair. In some embodiments, the detectable signal may beabsorbance of light having a particular wavelength or wavelength range.In some cases, the signal may be a color change that results, forexample, from the action of an enzyme/suppressor pair or anenzyme/cofactor pair on a substrate to form a detectable product. Insome embodiments, the detectable signal may be radiation, such as from aradiolabel. One of ordinary skill in the art would be able to identifyand implement other suitable detectable signals.

In some embodiments, the target nucleic acid may be quantified as instep 150. In some embodiments, quantification may be achieved using astandard curve for target nucleic acid concentration versus detectablesignal generated, for example, using the fluorescence values of a set ofsolutions that contained a range of known concentrations of targetnucleic acid combined with a binding agent comprising a signaling moietyand plotting the fluorescence values against the known concentrations oftarget nucleic acid. In some embodiments, for each solution containing aknown concentration of target nucleic acid, the methods as describedabove are performed to immobilize the binding agent with respect to thetarget nucleic acid, and the signaling moiety is then detected. Fittinga curve to the resultant plot, using a method such as a linearregression, can allow the derivation of a general mathematical formulafor calculating the concentration of target nucleic acid in a samplehaving an unknown concentration of target nucleic acid by inputting thedetectable signal value of the sample, after the binding agent has beenimmobilized with respect to the target nucleic acid, into the formula.

In another embodiment, a physical property of the signaling moiety maybe used to determine the concentration of a target nucleic acid. Forexample, the molar absorptivity and quantum yield of a fluorescentsignaling moiety at a particular wavelength may be used to determine theconcentration of target nucleic acid in solution using techniques knownto those skilled in the art. Generally, the fraction of target nucleicacid having binding agent immobilized thereto would be determined andfactored into the quantification. The concentration of the targetnucleic acid in a sample having an unknown concentration of the targetnucleic acid can be determined using the molar absorptivity and quantumyield by measuring the fluorescence of the sample at the wavelength thatcorresponds to the molar absorptivity and quantum yield as understood bythose skilled in the art.

In certain embodiments, the techniques and systems employed according tothe invention for the methods described herein allow rapid analysis orquantification of a target nucleic acid. For example, a method thatincludes steps 120, 130, 140, and 150 may be completed within 10seconds, within 30 seconds, within 1 minute, within 2 minutes, within 5minutes, within 10 minutes, within 20 minutes, within 30 minutes, within45 minutes, or within 1 hour. In some cases, a method that includessteps 120, 130, and 140 may be completed in between 10 seconds and 1hour, between 10 seconds and 30 minutes, between 10 seconds and 5minutes, between 10 seconds and 2 minutes, or between 10 seconds and 1minute.

In some embodiments, analysis of a target nucleic acid may allowquantification of a small amount of target nucleic acid. For instance,the methods may be capable of quantifying less than 100 ng, less than 50ng, less than 20 ng, less than 10 ng, less 5 ng, less than 2 ng, lessthan 1 ng, less than 100 pg, less than 10 pg, less than 1 pg, less than100 fg, less than 10 fg, or less than 1 fg of target nucleic acid. Insome cases, the methods may be capable of quantifying between 1 ng and100 ng, between 10 pg and 20 ng, or between 1 fg and 5 ng of targetnucleic acid. In some examples, the methods may be capable ofquantifying between 1 ng/microliter and 50 ng/microliter, between 1pg/microliter and 10 ng/microliter, or between 1 fg/microliter and 5ng/microliter of target nucleic acid. In some embodiments, the methodsmay be capable of quantifying fewer than 10⁵ molecules, between 10⁵ and10¹⁵ molecules, between 10⁵ and 10¹² molecules, between 10⁵ and 10¹¹molecules, between 10⁵ and 10¹⁰ molecules, or between 10⁵ and 10⁹molecules. In some embodiments, the quantification may be accomplished,even for samples containing native target nucleic acids at lowconcentration (e.g. certain forensic samples) without the need toamplify the target nucleic acid. Of course, analysis or quantificationof target nucleic acid detection in amounts and/or concentrationsoutside of these ranges may be accomplished by one or ordinary skill inthe art.

In certain embodiments, the target nucleic acid may be analyzed in asmall volume of solution. In certain embodiments, performing theanalysis in a microfluidic system may be advantageous for reducing thevolume of solution for performing the analysis. In some cases, thedetection may be carried out in less than 1 mL of solution, less than100 microliters of solution, less than 10 microliters of solution, lessthan 1 microliter of solution, less than 100 nanoliters of solution,less than 10 nanoliters of solution, or less than 1 nanoliters ofsolution. In some embodiments, by using a small volume of solution, theanalysis can be performed much more rapidly than when using a largervolume of solution. Thus, performing the analysis in a microfluidicsystem can be advantageous for quantifying a target nucleic acid withina short period of time (i.e., within 1 hour or even less as describedelsewhere herein).

As discussed above, in some embodiments, it may be advantageous toperform the methods in a microfluidic system. In some, but not allembodiments, all components of the systems and methods described hereinare microfluidic. Examples of suitable microfluidic systems aredescribed in International Patent Application Publication No.WO/2008/124104, entitled “Integrated Nucleic Acid Analysis,” filed Apr.4, 2008, by Tan et al., and U.S. Patent Application Publication No.2006/0260941, entitled “Ruggedized Apparatus for Analysis of NucleicAcid and Proteins,” filed May 19, 2005, by Tan et al., which areincorporated by reference herein. “Microfluidic,” as used herein, referschannels with at least one dimension less than 1 millimeter. The term“microfluidic devices” or “biochip” generally refers to devicesfabricated, for example by using semiconductor manufacturing techniques,to create structures that can manipulate tiny volumes (e.g. microliter,nanoliter or picoliter) of liquid, replacing macroscale analyticalchemistry equipment with devices that could be hundreds or thousandstime smaller and more efficient. For example, the channels of a biochipmay have cross-sectional dimensions ranging from 127 microns×127 micronsto 400 microns×400 microns and reservoirs may range from 400 microns×400microns in cross section to 1.9 mm×1.6 mm. In some embodiments, channelsand/or reservoirs may extend for distances as short as 0.5 mm to several10s of millimeters (e.g., greater than 20 mm, greater than 30 mm,greater than 40 mm, or greater than 50 mm).

In some embodiments, the microfluidic system may be an automated systemthat reduces the need for human intervention. An automated system may beadvantageous for reducing the quantification time of a target nucleicacid. For example, an automated microfluidic system may be capable ofperforming one or more steps automatically eliminating or reducing theneed for user intervention, and thus reducing the time for performingthe one or more steps. Thus, automation may contribute, in someembodiments, to the ability to quantify a target nucleic acid within 1hour or even less as described elsewhere herein.

In some embodiments, the quantification methods described herein may beperformed on a target nucleic acid before performing another procedureon the sample. For example, the quantification may be performed on thetarget nucleic acid before a reaction on the target nucleic acid (e.g.,an amplification reaction). Other examples of procedures include nucleicacid purification, nucleic acid amplification (e.g. both singleplex andmultiplex end-point PCR, real-time PCR, and reverse transcription PCR),post amplification nucleic acid cleanup, nucleic acid sequencing,nucleic acid ligation, nucleic acid hybridization, SNP analyses, andelectrophoretic separation. In some cases, one or more procedures may beperformed on a target nucleic acid using the same microfluidic system.For example, PCR and quantification of the target nucleic acid may beperformed using the same microfluidic system. In some embodiments, aprocedure may be performed in an active area of microfluidic system. Insome cases, a microfluidic system may contain one or more active areas.In some instances, each procedure may be performed in a separate activearea. In some embodiments, an active area may be used for one or moreprocedures. For example, an active area may be used for mixing a sampleand a binding agent and may be used for determining the sample (i.e.,the active area may be both a mixing region and a detector region). Inanother example, at least one of the active areas of the microfluidicdevice may comprise an area configured to amplify nucleic acid viapolymerase chain reaction (PCR). In some embodiments, an amplifying stepmay occur in an active area configured to amplify nucleic acid.

In some embodiments, the quantification methods described herein mayprovide feedback for adjusting a parameter of the sample. For example,the results of target nucleic acid quantification may indicate whetheror not to dilute or concentrate the sample. The results of targetnucleic acid quantification may also indicate to what extent to diluteor concentrate the sample. In some embodiments, the results of targetnucleic acid quantification may be used in an automated system to allowa precise quantity of nucleic acids to be utilized for subsequentprocessing. In some cases, quantification may be performed multipletimes on a given sample, for example, before and after other processingsteps. In some cases, different volumes of the sample can be routed todifferent regions of the biochip to allow parallel processing of thesample following a single quantification step (e.g., based onquantification, different amounts of target nucleic acid can be meteredfor subsequent processing such as PCR, SNP analysis, or DNA sequencing).

In some embodiments, the biochip may comprise a plurality ofmicrofluidic channels and active areas for sample manipulation. In someembodiments, the method may comprise a step after the quantifying step,where a selected quantity of the sample fluid may be directed to anactive area of the biochip. In some embodiments, the selected quantitymay be determined, at least in part, based on the results of thequantifying step.

In some embodiments, it may be desirable to control the amount of targetnucleic acid subjected to a procedure such as PCR amplification. Asdescribed above, in some embodiments, control of the amount of targetnucleic acid can be achieved by quantifying the target nucleic acid andthen metering out the desired amount of target nucleic acid to besubjected to a procedure. However, in some embodiments, a procedure maybe performed on a target nucleic acid before quantification or withoutquantifying the target nucleic acid. For example, in some embodiments,PCR amplification of a target nucleic acid may be performed withoutfirst quantifying the target nucleic acid. In some embodiments, thetarget nucleic acid may be purified from a sample to produce areproducible quantity of purified target nucleic acid. For example, theamount of target nucleic acid can be controlled by using a “cut-off”approach. In this approach, a binding membrane may be used that can binda target nucleic acid up to a threshold amount, above whichsubstantially no additional target nucleic acid is bound (i.e., thebinding membrane may have a defined nucleic acid binding capacity).Generally, binding of a target nucleic acid to the binding membranecomprises contacting at least a portion of the sample with the bindingmembrane to bind the target nucleic acid. In some embodiments, thenucleic acid binding capacity is essentially the same as thereproducible quantity of purified target nucleic acid.

In some embodiments, sample amounts can be chosen such that the range oftarget nucleic acid amounts contained in the samples is above thebinding membrane threshold amount, such that substantially all targetnucleic acid in an amount greater than the binding membrane thresholdamount is not retained by the binding membrane. Thus, the amount oftarget nucleic acid can be controlled without quantification for asample containing an unknown amount of target nucleic acid butcontaining an amount of target nucleic acid above the binding membranethreshold amount. Such an approach may be advantageous, for example, fordecreasing the time needed to perform a procedure by eliminating aquantification step.

In some cases, the binding membrane may contain one or more layers. Insome embodiments, the amount of nucleic acid bound by the bindingmembrane (i.e., binding capacity) scales substantially linearly with thenumber of layers in the binding membrane. In some embodiments, thebinding capacity scales with the diameter of the binding membrane. Thediameter of the binding membrane may be, for example, at least 0.1 mm,at least 0.5 mm, at least 1 mm, at least 2 mm, at least 5 mm, or atleast 10 mm. In some embodiments, the binding membrane may be a silicamembrane capable of binding a nucleic acid. As a non-limiting example,FIG. 12 shows the binding performance of a 1 mm diameter bindingmembrane over a range of DNA inputs.

In some embodiments, the binding membrane threshold amount (i.e.,saturation amount) may be at least 50 ng, 100 ng, at least 200 ng, atleast 300 ng, at least 400 ng, at least 500 ng, at least 600 ng, atleast 700 ng, at least 800 ng, or even more. In some embodiments, thebinding efficiency of the binding membrane may be less than 100% suchthat an excess of target nucleic acid may be needed to saturate thebinding membrane. For example, at least 10% more, at least 20% more, atleast 50% more, at least 100% more, or at least 200% more target nucleicthan the binding membrane threshold amount may be needed to saturate thebinding membrane.

The target nucleic acid may be eluted from the binding membrane usingany suitable method. For example, the target nucleic acid may be elutedby flowing a fluid through the binding membrane having a pH within aparticular range or a salt concentration within a particular range.Other suitable methods will be known to those of ordinary skill in theart.

In some embodiments, a quantification assay can be conducted in amicrofluidic biochip designed to be compatible with all the requiredprocess steps. This can be advantageous, for example, in a humanforensic identification casework biochip, where a portion of thepurified DNA solution may be directed to the quantification module, andthe remaining DNA may be available for aliquoting, for example, for STRamplification. A central feature of the approach is that thequantification data may be utilized to define the volume to be subjectedto amplification. Depending on the application, the precise volume or anapproximate volume would be metered microfluidically. For example, ifthe elution volume of the purified DNA is 100 μL and the volume of DNAsolution utilized for quantification is approximately 1 μL, the majorityof the DNA will be available for STR amplification. In some embodimentsin which the quantity of nucleic acids is known to be small but theprecise quantity is unknown (e.g. forensic touch samples), 10% or moreof the eluted DNA can be utilized for quantification.

In some embodiments, the quantification method may be performed using amicrofluidic system. The microfluidic system may allow the samplecontaining the target nucleic acid, the binding agent, and otherreagents to be flowed through the biochip. For example, a single biochipmay have a region for PCR amplification, fragment separation anddetection, nucleic acid sequencing, ultrafiltration, and nucleic acidquantification. In some embodiments, this multifunctional biochip mayprocess one or more samples in parallel. In some embodiments, the samplemay be flowed to one or more regions in the biochip where one or moreprocedures may be performed. The sample may be flowing or stationarywhere one or more of the procedures is performed. For example, althoughthe sample is contained in a microfluidic device, it may not necessarilyin certain embodiments be flowing when the detection is performed.

In some cases, two or more procedures may be performed on the sample inthe same region. In some embodiments, the biochips described below mayallow integration of target nucleic acid quantification with one or moreother procedures, as noted above. Accordingly, an almost limitlessnumber of combinations can be designed into the biochip, allowing acomplex set of manipulations to be completed on the biochip. One skilledin the art will appreciate that the biochips of the invention can bedesigned to perform a multitude of different types of analysis withessentially limitless process complexity.

The “cross-sectional dimension” of the channel is measured perpendicularto the direction of fluid flow. Most fluid channels in components of theinvention have maximum cross-sectional dimensions less than 2 mm, and insome cases, less than 1 mm. In one set of embodiments, all fluidchannels containing embodiments of the invention are microfluidic orhave a largest cross sectional dimension of no more than 2 mm or 1 mm.In another embodiment, the fluid channels may be formed in part by asingle component (e.g. an etched substrate or molded unit). Of course,larger channels, tubes, chambers, reservoirs, etc. can be used to storefluids in bulk and to deliver fluids to components of the invention. Inone set of embodiments, the maximum cross-sectional dimension of thechannel(s) containing embodiments of the invention are less than 500microns, less than 200 microns, less than 100 microns, less than 50microns, or less than 25 microns.

A “channel,” as used herein, means a feature on or in an article(substrate) that at least partially directs the flow of a fluid. Thechannel can have any cross-sectional shape (circular, oval, triangular,irregular, square or rectangular, or the like) and can be covered oruncovered. In embodiments where it is completely covered, at least oneportion of the channel can have a cross-section that is completelyenclosed, or the entire channel may be completely enclosed along itsentire length with the exception of its inlet(s) and outlet(s). Achannel may also have an aspect ratio (length to average cross sectionaldimension) of at least 2:1, more typically at least 3:1, 5:1, or 10:1 ormore. An open channel generally will include characteristics thatfacilitate control over fluid transport, e.g., structuralcharacteristics (an elongated indentation) and/or physical or chemicalcharacteristics (hydrophobicity vs. hydrophilicity) or othercharacteristics that can exert a force (e.g., a containing force) on afluid. The fluid within the channel may partially or completely fill thechannel. In some cases where an open channel is used, the fluid may beheld within the channel, for example, using surface tension (i.e., aconcave or convex meniscus).

The channel may be of any size, for example, having a largest dimensionperpendicular to fluid flow of less than about 5 mm or 2 mm, or lessthan about 1 mm, or less than about 500 microns, less than about 200microns, less than about 100 microns, less than about 60 microns, lessthan about 50 microns, less than about 40 microns, less than about 30microns, less than about 25 microns, less than about 10 microns, lessthan about 3 microns, less than about 1 micron, less than about 300 nm,less than about 100 nm, less than about 30 nm, or less than about 10 nm.In some cases the dimensions of the channel may be chosen such thatfluid is able to freely flow through the article or substrate. Thedimensions of the channel may also be chosen, for example, to allow acertain volumetric or linear flow rate of fluid in the channel. Ofcourse, the number of channels and the shape of the channels can bevaried by any method known to those of ordinary skill in the art. Insome cases, more than one channel may be used. For example, two or morechannels may be used, where they are positioned inside each other,positioned adjacent to each other, positioned to intersect with eachother, etc.

The microfluidic chips (i.e., biochips) of the invention can beprimarily composed of plastics. Useful types of plastics include, butare not limited to: unsaturated, partially unsaturated or saturatedcyclic olefin copolymers “COC,” unsaturated, partially unsaturated, orsaturated cyclic olefin polymers “COP,” poly(methyl)methacrylate “PMMA,”polycarbonate “PC,” polypropylene “PP,” polyethylene “PE,”polyetheretherketone “PEEK,” poly(dimethylsiloxane) “PDMA,” andpolyimide “PI.” The term “poly(methyl methacrylate)” or “PMMA,” as usedherein, means the synthetic polymers of methyl methacrylate, includingbut not limited to, those sold under the tradenames Plexiglas™,Limacryl™, R-Cast™, Perspex™, Plazcryl™ Acrylex™, ACrylite™,ACrylplast™, Altuglas™, Polycast™, and Lucite™, as well as thosepolymers described in U.S. Pat. Nos. 5,561,208, 5,462,995, and5,334,424, each of which are incorporated herein by reference. In someembodiments, a plastic having a glass transition temperature greaterthan that of the maximal temperature to be utilized in the amplificationreaction may be selected. Any number of these processes and materialscan be used to fabricate the biochips described herein. In someembodiments, including injection molding, hot embossing, and/ormachining may be used. For example, the biochips can be prepared byinjection molding of a plastic substrate, for example, a COC or COPbased polymers (currently sold under the tradenames Topas™, Zeonex™Zeonor™, and Apel™). In this fabrication methodology, an injection moldand mold insert consisting of the negative of the features to be formedmay be fabricated by machining and subsequent surface polishing.Together, the mold and insert may allow the substrate layers to befabricated and the formed substrate to comprise the channels, reactionchamber features and vias. In some embodiments, the substrate and coverlayers can be diffusion bonded by the application of heat and pressure.Injection molded parts may comprise gross features (such as fluidreservoirs) and/or fine features (such as capillary valves). In somecases, it can be preferable to create fine features on one set of partsand larger features on another set, because the approaches to injectionmolding of these differently-sized features can vary. For largereservoirs (measuring several mm (about 1-50 mm) on a side and withdepths of several mm (about 1-10 mm) and capable of accommodating up toor more than hundreds of microliters), conventional molding can beemployed using machined injection molding tools. In some embodiments,the tools can be burned into steel or other metal using a graphiteelectrode that has been machined to be a negative of the tool. Moreinformation about materials and fabrication methods are contained inU.S. Patent Application Publication No. 2009/0023603, entitled “Methodsfor Rapid Multiplexed Amplification of Target Nucleic Acids,” filed Apr.4, 2008, by Selden et al., which is incorporated herein by reference.

In some embodiments, a microfluidic system may include an instrument anda microfluidic chip (i.e., a biochip), where the microfluidic chip isassociated with the instrument. In various embodiments, the biochip mayhave a plurality of features integrated into the biochip. For example, abiochip may comprise components that facilitate sample insertion;removal of foreign matter; removal of interfering nucleic acids;concentration of cells of interest; amplification of nucleic acids;thermal cycling; mixing of fluids; detection of signaling moieties; etc.In some embodiments, a pre-processing component of the biochip mayaccept a sample, performs initial removal of particulates and foreignnucleic acid containing cells, and concentrate the cells of interestinto a small volume. In some embodiments, a sample tube may be used thatcan accept a swab. The sample tube, for instance, may be filled withlysis solution to perform the lysis and extraction step. As discussedabove, the swab can be placed in contact with a number ofcell-containing sites, including a bloodstain, a fingerprint, water, anair filter, or a clinical site (e.g., buccal swab, wound swab, nasalswab).

In some embodiments, the biochip may include a particulate filter, apurification filter, beads, or other materials.

A variety of lysis and extraction methods can be employed as describedin more detail above. In some embodiments, lysis and extraction can beperformed on a sample containing 10⁶ cells or less. Depending on theapplication, a smaller number of starting cells can be utilized in thebiochips and methods of the invention, less than 10⁵, less, than 10⁴,less than 10³, less than, 10², less than 10, and, in cases whenmulti-copy sequences are to be analyzed, less than 1.

In some embodiments, nucleic acid purification can be achieved byinserting a purification medium between an input and output channel. Insome cases, the purification medium can be silica fiber based and usechaotropic-salt reagents to lyse the biological sample, expose thetarget nucleic acid, and bind the target nucleic acid to thepurification media. The lysate may then be transported via the inputchannel through the purification medium to bind the nucleic acids. Insome embodiments, bound nucleic acid may be washed by an ethanol basedbuffer to remove contaminants. In some cases, this can be accomplishedby flowing wash reagents via the input channel through the purificationmembrane. In some instances, bound nucleic acid may be then eluted fromthe membrane by flowing an appropriate buffer (e.g., a low salt buffer).Other solid phases will be known to those of ordinary skill in the art.Essentially, any nucleic acid purification method that is functional ina conventional setting can be adapted to the biochip.

In some embodiments, the biochip may also contain different componentsfor integrating the functional modules. These modules involve, forexample, the transport of liquids from point to point on the biochip,the control of flow rates for processes that may be flow-rate dependent,(e.g., washing steps, particle separation, and elution), the gating offluid motion in time and space on the biochip (e.g., through the use ofsome form of valve), and the mixing of fluids.

A variety of methods can be used for fluid transport and controlledfluid flow. One exemplary method is positive-displacement pumping, wherea plunger in contact with either the fluid or an interposing gas orfluid drives the fluid a precise distance based on the volume displacedby the plunger during the motion. An example of such a method is asyringe pump. Another exemplary method is the use of integratedelastomeric membranes that are pneumatically, magnetically, or otherwiseactuated. In some embodiments, these membranes can be used as valves tocontain fluids in a defined space and/or prevent premature mixing ordelivery of fluids. In some cases, when used in series, these membranescan form a pump analogous to a peristaltic pump. For example, bysynchronized, sequential actuation of membranes, fluid can be “pushed”from its trailing side as membranes on the leading side are opened toreceive the moving fluid (and to evacuate any displaced air in thechannels of the device). Yet another method for driving fluids andcontrolling flow rates is to apply vacuum or pressure directly on thefluids themselves, by altering the pressure at the leading, trailing, orboth menisci of the fluid. Appropriate pressures (for example, in therange of 0.05-30 psi) may be applied. Flow rates also can be controlledby properly sizing the fluidic channels. Without wishing to be bound byany theory, the flow rate is proportional to the pressure differentialacross the fluid and the hydraulic diameter to the fourth power andinversely proportional to the length of the channel or the liquid plugand the viscosity. Other methods for fluid transport will be known tothose of ordinary skill in the art.

In some embodiments, fluid gating can be achieved using a variety ofactive valves. In some cases, an active value can include apiezoelectric valve or a solenoid valve that, in some instances, can bedirectly incorporated into the chip. In some embodiments, the valve maybe external to the chip but in fluid communication with ports on themain chip body. In some embodiments, passive valves, such as capillarymicrovalves, may be used. In some cases, microvalves can use, forexample, surface energy and/or geometric features such as sharp edges toimpede flow when the pressure applied to the fluid is below a criticalvalve.

Mixing can be accomplished in a variety of ways. In some embodiments,diffusion can be used to mix fluids, for example, by co-injecting thetwo fluids into a single channel or chamber. In some embodiments, mixingcan be enhanced. For example, techniques such as lamination may be used,in which the fluid stream is divided and recombined one or more times.In another embodiment, chaotic advection within the flow channel can becreated, for example, through the use of microstructure within thechannel. In systems using active pumps and valves, mixing can beaccomplished by cycling fluid between two points on the device multipletimes.

An exemplary integrated biochip is shown in FIG. 2 . The deviceintegrates the functions of reagent distribution and metering; mixing ofreagents with samples; delivery of samples to a thermal cycling portionof the chip; and thermal cycling. This exemplary biochip has severalfunctional regions that perform PCR amplification (101), Sangersequencing (102), and ultrafiltration (103), and quantification (104).Individual samples (containing unpurified, partially purified, orpurified DNA) may be transferred to sample input ports (105). PCRreaction solution may be transferred to the biochip and mixed withsamples in the four amplification reaction chambers (within 101) viapneumatic pressure on the PCR reagent reservoir and channel (106).Following thermal cycling, the amplified samples may be transported(again by pneumatic pressure) to the sequencing chambers of region 102.In some instances, sequencing reaction solution (e.g., Sanger sequencingreaction solution) may be transferred to the biochip and mixed with thefour amplified samples via pneumatic pressure on the sequencing reagentreservoir and channel (107). Following cycle sequencing, the samples maybe transported to region 103 for ultrafiltration. As the sequencedmaterial is fluorescently labeled, quantification can be performed inregion 104. In this case, quantification can be utilized to ensure anappropriate amount of material is loaded into a subsequent separationand detection process.

In some embodiments, following optional DNA purification, the DNAsolution may be transferred to a chamber for mixing with the bindingagent, and transferred to a channel, region or chamber forquantification, optionally without prior amplification. In some cases,following quantification, purified DNA would be metered for subsequentprocessing. In some embodiments, the samples (e.g., test fluids) may bedelivered to an analysis chamber. In some embodiments, the test fluidmay be located in a detector region e.g. region 104. In some cases, thetest fluid may be flowing or stationary. For example, the method maycomprise a locating step comprising flowing the test fluid to thedetector region in the microfluidic channel. In another example, themethod may comprise a locating step comprising flowing the test fluidthrough the detector region of the microfluidic channel duringdetection. The analysis chamber or detector region may, in someinstances, be in thermal cycling portion of the chip. In someembodiments, the locating step may comprise maintaining the test fluidstationary at a region and moving a detector into alignment with theregion to transform the region into the detector region.

As discussed above, the system may comprise a thermal cycling function.The thermal cycling function may capable of cycling between two or moretemperatures. For example, the thermal cycling function may be capableof heating and cooling. In some cases, the thermal cycling function canchange the temperature of a sample in the thermal cycling portion of thebiochip rapidly. For example, the thermal cycling function may becapable of changing the temperature of the sample at a rate of 1°C./second, 5° C./second, 10° C./second, 20° C./second, 30° C./second,50° C./second, 100° C./second, or 200° C./second. The thermal cyclingfunction may also be capable of holding the temperature of the sample ata particular temperature for a period of time.

In some embodiments, the analysis chamber may be fabricated between aninput and an output channel. In some cases, the system may allow asample to be flowed through the analysis chamber. In some embodiments,the analysis chamber may be in proximity to a detection system fordetecting the detectable signal of the signaling moiety in the analysischamber. For example, in some embodiments, the analysis chamber may bein proximity to an optical excitation and detection system to allowfluorescence from the sample to be measured.

In some embodiments, the system comprises an excitation and/or detectionsubsystem for interacting with a sample. In some embodiments, theexcitation subsystem comprises one or more excitation sources. In someembodiments, the excitation subsystem comprises an excitation beam pathwith optical elements including, but not limiting to, lenses, pinholes,mirrors and objectives, to condition and/or focus the excitation sourcein an excitation/detection window. In some embodiments, opticalexcitation of a sample can be accomplished by one or more lasers (e.g.,a dual laser system). In some cases, the laser emission wavelength maybe in the visible region, e.g., between 400 to 650 nm. For example,solid state lasers can provide emission wavelengths of approximately 460nm, 488 nm, and 532 nm. These lasers include, for example, the Compass,Sapphire, and Verdi products from Coherent (Santa Clara, Calif.). Gaslasers can include argon-ion and helium neon with emission in thevisible wavelengths at approximately 488 nm, 514 nm, 543 nm, 595 nm, and632 nm. Other lasers with emission wavelengths in the visible region areavailable from CrystaLaser (Reno, Nev.). In one embodiment, a 488 nmsolid state laser Sapphire 488-200 (Coherent, Santa Clara, Calif.) canbe utilized. In another embodiment, a light source with wavelengthbeyond the visible range can be used for exciting dyes having absorptionand/or emission spectra beyond the visible range (e.g., infrared orultra-violet emitting dyes). Alternatively, optical excitation can beachieved by the use of non-laser light sources with emission wavelengthsappropriate for dye excitation, including light emitting diodes, andlamps.

In some embodiments, the detection subsystem comprises one or moreoptical detectors, a wavelength dispersion device (which performswavelength separation), and one or a series of optical elementsincluding, but not limited to, lenses, pinholes, mirrors and objectivesto collect emitted fluorescence from signaling entity present at theexcitation/detection window. The fluorescence emitted can be from asingle dye or a combination of dyes. In order to discriminate the signalto determine its contribution from the emitting dye, wavelengthseparation of the fluorescence can be utilized. This can be achieved,for example, by the use of dichroic mirrors and bandpass filter elements(available from numerous vendors including Chroma, Rockingham, Vt.). Inthis configuration, the emitted fluorescence passes through a series ofdichroic mirrors where one portion of the wavelength will be reflectedby the mirror to continue traveling down the path, and the other portionwill pass through. A series of discrete photodetectors, each onepositioned, for example, at the end of the dichroic mirror can be usedto detect light over a specific range of wavelengths. In someembodiments, a bandpass filter can be positioned between the dichroicmirror and photodetector to further narrow the wavelength range prior todetection. Optical detectors that can be utilized to detect thewavelength-separated signals include photodiodes, avalanche photodiodes,photomultiplier modules, and charge-coupled device (CCD) cameras. Theseoptical detectors are available from suppliers such as Hamamatsu(Bridgewater, N.J.).

In certain embodiments, it may be advantageous to use a single opticaltrain for both quantification and laser induced fluorescence detection.For example, by using given optical components for two or morefunctions, it is possible to reduce the volume, weight, and cost of theinstrument. A single optical train may comprise optical elements thatcouple the excitation source to the optical interrogation chambers ofthe quantification module and the excitation/detection window of theseparation and detection module. In some embodiments, the optical trainmay also couple the light from the optical interrogation chambers (i.e.,analysis chambers) of the quantification module and theexcitation/detection window of the separation and detection modulethrough the wavelength separation element and to the optical detectors.In some embodiments, the optical elements include lenses, mirrors,dichroic mirrors, band pass filters, scanners, translation stages, lightsources, and/or detectors.

Generally, the optical train may accomplish one or more of the followingobjectives. In some cases, the optical train may maximize excitationefficiency by efficiently coupling the excitation source to the opticalinterrogation chamber. In some cases, the optical train may maximizeexcitation efficiency by efficiently coupling the excitation source tothe excitation/detection window of the separation and detection module.In some cases, the optical train may maximize fluorescence collectionefficiency by minimizing losses between the optical interrogationchamber and the detector. In some cases, the optical train may maximizefluorescence collection efficiency by minimizing losses between theexcitation/detection window and the detector. In some cases, the opticaltrain may minimizing the number of optical elements by maximizing thenumber of shared elements between the excitation path and the detectionpaths. In some cases, the optical train may minimize number of opticalcomponents by maximizing the number of shared elements between thequantification module and the separation and detection module. In somecases, the optical train may use a single laser for excitation of thequantification module and the separation and detection module. In somecases, the optical train may use a common wavelength separation anddetector module for the microfluidics quantification and microfluidicseparation and detection modules. In some cases, the optical train mayuse commercially available components and select components that canwithstand the vibration of transport and wide variations in temperature.

FIGS. 3 and 4 show a schematic of an embodiment of an optical trainconfiguration for both microfluidics quantification and separation anddetection. The excitation path comprises a laser source (201), shortpass dichroic mirror (202), a translation mirror (209), and a fixedmirror (208) pair that can allow the beam path to be directed to thequantification or the separation and detection portion of the biochip.In instances when the translation mirror (209) is in the quantificationposition, the excitation beam may be directed to a lens (203), a firstscanning mirror (205), and a lens and objective assembly (204). Thescanning mirror (205) may direct the excitation beam to each of thequantification channels (206) within the biochip. Alternatively, withthe translation mirror (209) in the separation and detection position,the excitation beam may be directed to a lens (203 b), a second scanningmirror (205 b), and a lens and objective assembly (204 b). The secondscanning mirror (205 b) may direct the excitation beam to each of theseparation and detection channels (207) within the biochip. In thisconfiguration, the laser source (201) is common to the quantificationand separation and detection beam paths. Alternative optical excitationsources to the laser include LEDs and lamps.

The detection beam path may comprise the wavelength separation anddetection element (211), a pinhole (210), and a lens (203). Thedetection beam path and excitation beam path may share common elementsfrom the dichroic mirror (202) to the quantification channels (206) andfrom the dichroic mirror (202) to the separation and detection channels(207). The wavelength separation element may include a set of dichroicmirrors and bandpass filters to separate the wavelength components ofthe incoming fluorescence. These can either be discrete elements or theycan be integrated in a single subassembly. Alternatively, wavelengthseparation can be achieved with a spectrograph or a prism. The detectionelements include PMTs which can be discrete or integrated modules withmultiple anodes. In this optical train configuration, the wavelengthseparation and detection module (211) may be common to quantificationand the separation and detection modules.

In this optical train, a translation mirror (209) and fixed mirror (208)may be used to set the excitation and detection beam path formicrofluidic quantification or microfluidic separation and detection.Channel to channel selection for microfluidic quantification may beachieved with the first scanning mirror (205), and channel to channelselection for microfluidic separation and detection may be achieved witha second scanning mirror (205 b). The schematic of FIG. 3 shows theoptical train configured to excite and interrogate the quantificationchambers. The schematic of FIG. 4 shows the optical train configured toexcite and detect from the separation and detection channels of theseparation and detection module.

FIGS. 5 and 6 show schematics of an alternate optical train that can beused for both microfluidic quantification and separation and detection.The excitation path comprises of a laser source (201), short passdichroic mirror (202), a translation mirror (209), and a fixed mirror(208) pair that allows the beam path to be directed to thequantification or the separation and detection portion of the biochip.In instances when the translation mirror (209) is in the quantificationposition, the excitation beam may be directed to a lens (203 c) and afirst and second mirror (205 c and 205 d). The beam may then be directedto a translation mirror assembly (212). This assembly includes a mirrorthat may be mounted on a programmable translation stage. The translationmirror assembly (212) can direct the excitation beam to each of thequantification chambers (206) within the biochip. Alternatively, withthe translation mirror (209) in the separation and detection position,the excitation beam may be directed to a lens (203 b), a second scanningmirror (205 b), and a lens and objective assembly (204 b). The secondscanning mirror (205 b) may direct the excitation beam to each of theseparation and detection chambers (207) within the biochip. In thisconfiguration, the laser source (201) may be common to thequantification and separation and detection beam paths. Alternativeoptical excitation sources include LEDs and lamps.

The detection beam path comprises the wavelength separation anddetection element (211), a pinhole (210), and a lens (203). Thedetection beam path and excitation beam path may share common elementsfrom the dichroic mirror (202) to the quantitation channels (206) andfrom the dichroic mirror (202) to the separation and detection channels(207). The wavelength separation element includes a set of dichroicmirrors and bandpass filters to separate the wavelength components ofthe incoming fluorescence. These can either be discrete elements or theycan be integrated in a single subassembly. Alternatively, wavelengthseparation can be achieved with a spectrograph or a prism. The detectionelements include PMTs which can be discrete or integrated modules withmultiple anodes. In this optical train configuration, the wavelengthseparation and detection module (211) may be common to quantificationand the separation and detection modules.

In this optical train, a translation mirror (209) and fixed mirror (208)may be used to set the excitation and detection beam path formicrofluidic quantification or microfluidic separation and detection.Channel to channel selection for microfluidic quantification may beachieved with the translation mirror assembly (212), and channel tochannel selection for microfluidic separation and detection may beachieved with a scanning mirror (205 b). The schematic of FIG. 5 showsthe optical train configured to excite and interrogate thequantification chambers. The schematic of FIG. 6 shows the optical trainconfigured to excite and detect from the separation and detectionchannels of the separation and detection module.

A third approach is the use of a miniaturized excitation source whichcan be a laser, LED, or lamp, a wavelength separation element, and adetector, all of which may be mounted on a translation stage (213) (FIG.7 ). The translation stage can allow each of the quantification channels(206) to be interrogated. In this approach, excitation, wavelengthseparation and detection module for the quantification system may beindependent of the separation and detection system. The optical trainfor separation and detection can include the elements described in FIGS.3, 4, 5, and 6 .

A fourth approach for the interrogation of the quantification channelsis to simultaneously excite all the quantification chambers with alaser, LED, or lamp. Fluorescence from all the quantification chambersmay be collected by a lens and passed through a diffraction element tospatially separate the wavelength components of the fluorescence. Thismay be then imaged onto a CCD camera or a 2-dimensional detector array.In this configuration, one axis of the detector array can correlate tochannels of the quantification chambers, and the other axis of thedetector array can correlate with the fluorescence wavelength. Theoptical train for separation and detection can include the elementsdescribed in FIGS. 3, 4, 5, and 6 . In this configuration, theexcitation source can be common for both the quantification andseparation and detection modules.

In one embodiment, wavelength components are separated by the use ofdichroic mirrors and bandpass filters and these wavelength componentsare detected with Photomultiplier Tube (PMT) detectors (H7732-10,Hamamatsu). The dichroic mirror and bandpass components can be selectedsuch that incident light on each of the PMTs consists of a narrowwavelength band corresponding to the emission wavelength of thefluorescent dye. The band pass may be selected to be centered about thefluorescent emission peak with a band pass of wavelength range ofbetween 1 and 50 nm. The system may be capable of one, two, three, four,five, six, seven, or even eight color detection and can be designed withone, two, three, four, five, six, seven, or even eight PMTs and acorresponding set of dichroic mirrors and bandpass filters to divide theemitted fluorescence into eight distinct colors. More than eight dyescan be detected by applying additional dichroic mirrors, bandpassfilters and PMT. FIG. 8 shows a beam path for discrete bandpass filterand dichroic filter implementation, according to one embodiment. Anintegrated version of this wavelength discrimination and detectionconfiguration is the H9797R, Hamamatsu, Bridgewater, N.J.

Another method of discriminating the dyes that make up the fluorescencesignal involves the use of wavelength dispersive elements and systemssuch as prisms, diffraction gratings, transmission gratings (availablefrom numerous vendors including ThorLabs, Newton, N.J.; and Newport,Irvine, Calif.; and spectrographs (available from numerous vendorsincluding Horiba Jobin-Yvon, Edison, N.J.). In this embodiment, thewavelength components of the fluorescence may be dispersed over aphysical space. Detector elements placed along this physical space maydetect light and allow the correlation of the physical location of thedetector element with the wavelength. Exemplary detectors suitable forthis function include array-based and include multi-element photodiodes,CCD cameras, back-side thinned CCD cameras, multi-anode PMT. One skilledin the art will be able to apply a combination of wavelength dispersionelements and optical detector elements to yield a system that is capableof discriminating wavelengths from the dyes used in the system.

In another embodiment, a spectrograph may be used in place of thedichroic and bandpass filters to separate the wavelength components fromthe excited fluorescence. Details on an exemplary spectrograph designare available in John James, Spectrograph Design Fundamental. Cambridge,UK: Cambridge University Press, 2007. In some embodiments, thespectrograph P/N MF-34 with a concave holographic grating with aspectral range of 505-670 run (P/N 532.00.570) (HORIBA Jobin Yvon Inc,Edison, N.J.) may be used in this application. Detection can beaccomplished with a linear 32-element PMT detector array (H7260-20,Hamamatsu, Bridgewater, N.J.). In some embodiments, collectedfluorescence may be imaged on the pinhole, reflected, dispersed, andimaged by the concave holographic grating onto the linear PMT detectorthat is mounted at the output port of the spectrograph. In some cases,the use of a PMT-based detector takes advantage of the low dark noise,high sensitivity, high dynamic range, and rapid response characteristicof PMT detectors. In some embodiments, the use of a spectrograph andmulti-element PMT detector for detection of excited fluorescence allowsfor flexibility in the number of dyes and the emission wavelength ofdyes that can be applied within the systems and within the lane, withoutthe need for physically reconfiguring the detection system (i.e., thedichroic mirror, bandpass, and detector) of the instrument. In someembodiments, the data collected from this configuration may be awavelength dependent spectra across the visible wavelength range foreach scan for each lane. In some cases, generating a full spectrum perscan provides dye flexibility both in terms of dye emission wavelengthand number of dyes that can be present within a sample. In addition, theuse of the spectrometer and linear multi-element PMT detector also canallow for extremely fast read-out rates as all the PMT elements in thearray may be read-out in parallel. FIG. 9 shows the beam path formulti-element PMT and spectrograph implementation, according to oneembodiment.

In some embodiments, the instrument may employ a staring mode ofoperation to detect multiple lanes simultaneously and/or multiplewavelengths simultaneously. In one configuration, the excitation beammay be simultaneously impinged on all lanes at the same time. In someembodiments, the fluorescence may be collected by a two dimensionaldetector such as a CCD camera or array. For example, one dimension ofthe detector may represent the physical wavelength separation, while theother dimension may represent the spatial or lane-lane separation.

For simultaneous excitation and detection of multiple samples, ascanning mirror system may be utilized to steer both the excitation anddetection beam paths in order to image each of the lanes of the biochip.In this mode of operation, the scanning mirror steers the beam paths,scanning sequentially from lane to lane from the first lane to the lastlane, and the repeating the process again from the first lane to thelast lane again. A lane-finding algorithm may be used to identify thelocation of the lane.

An embodiment of an optical detection system for simultaneous multiplelane and multi dye detection is shown in FIG. 24 . The fluorescenceexcitation and detection system 40 excites the signaling moiety (e.g.,the signaling moiety of a binding agent comprising a signaling moietyimmobilized with respect to a target nucleic acid) by scanning an energysource (e.g., a laser beam) through a portion of each of themicrochannels while collecting and transmitting the induced fluorescencefrom the dye to one or more light detectors for recordation, andultimately analysis. In one embodiment, the fluorescence excitation anddetection assembly 40 includes a laser 60, a scanner 62, one or morelight detectors 64, and various mirrors 68, spectrograph, and lenses 72for transmitting a laser beam emitted from the laser 60 through opening42 to the test module 55 and back to the light detectors 64. The scanner62 moves the incoming laser beam to various scanning positions relativeto the test module 55. Specifically, the scanner 62 moves the laser beamto a pertinent portion of each micro channel within the test module 55to detect respective separate components. The multi element PMT 64(i.e., the light detector) collects data (e.g. the fluorescent signalsfrom DNA fragments of varying length) from the test module 55 andprovides the data electronically through a cable to a data acquisitionand storage system (not shown). In one embodiment, the data acquisitionand storage system can include a ruggedized computer available fromOption Industrial Computers (13 audreuil-Dorion, Quebec, Canada).

In some embodiments, a signal processing algorithm may be used tocorrect, filter, and/or analyze the data. This process may comprisesteps such as locating a callable signal, correcting the signalbaseline, filtering out noise, removing color cross-talk, and/oridentifying signal peaks. For example, locating the callable signal maybe performed by employing a threshold. This procedure may be used toremove extraneous data from the beginning and end of the signal. In someembodiments, the background may be removed from the signal, for example,so that the signal may have a common baseline for all detected colors.In some cases, a lowpass filter may be applied to remove high frequencynoise from the signal.

In one embodiment, a kit may be provided, containing one or more of theabove compositions. A “kit,” as used herein, typically defines a packageor an assembly including one or more of the compositions of theinvention, and/or other compositions associated with the invention, forexample, as previously described. Each of the compositions of the kitmay be provided in liquid form (e.g., in solution), in solid form (e.g.,a dried powder), etc. A kit of the invention may, in some cases, includeinstructions in any form that are provided in connection with thecompositions of the invention in such a manner that one of ordinaryskill in the art would recognize that the instructions are to beassociated with the compositions of the invention. For instance, theinstructions may include instructions for the use, modification, mixing,diluting, preserving, administering, assembly, storage, packaging,and/or preparation of the compositions and/or other compositionsassociated with the kit. The instructions may be provided in any formrecognizable by one of ordinary skill in the art as a suitable vehiclefor containing such instructions, for example, written or published,verbal, audible (e.g., telephonic), digital, optical, visual (e.g.,videotape, DVD, etc.) or electronic communications (including Internetor web-based communications), provided in any manner.

In this description terms such as “target nucleic acid”,“oligonucleotide,” “binding agent,” “nucleic acid,” “strand,” and otherlike terms in the singular. One of ordinary skill in the art willunderstand that many terms used to describe molecules may be used in thesingular and refer to either a single molecule or to a multitude. Forexample, although a target nucleic acid may be detected by a bindingagent in an assay, an assay may require many copies of binding agent andmany copies of target nucleic acid. In such instances, terms are to beunderstood in context. Such terms are not to be limited to meaningeither a single molecule or multiple molecules.

The following examples are intended to illustrate certain embodiments ofthe present invention, but do not exemplify the full scope of theinvention.

Example 1

This example describes the system used in the examples below.

The system comprises an instrument for separation and detection oflabeled DNA fragments and is described in more detail in U.S. PatentApplication Publication No. 2009/0023603, entitled “Methods for RapidMultiplexed Amplification of Target Nucleic Acids,” filed Apr. 4, 2008,by Selden et al., which is incorporated herein by reference. Theinstrument is ruggedized for field and laboratory use, has low powerconsumption, and is CE marked under the Low Voltage Directive 73/23/EEC.DNA separation takes place within a 16 sample biochip and custom sievingmatrix by applying appropriate loading, pullback, and separationvoltages through a high voltage subsystem. A laser induced fluorescencedetection subsystem excites and collects fluorescence from the labeledDNA fragments that pass through the excitation and detection zone of thebiochip. Separations carried out by applying a 150 V/cm and 300 V/cmelectric field along the separation channel are completed in 28 and 15minutes respectively providing fast separations with better than singlebase pair resolution and detecting the product of PCR amplifications ofsingle copy targets.

System configuration. The subsystems (pneumatic, thermal cycling, andseparation and detection subsystems) are controlled by a rack mountedruggedized industrial computer. This computer has the functionality of afull-sized desktop computer and includes a 17 inch LCD display, a fullsized keyboard, and mouse.

Fluid Manipulation Instrumentation. Fluid flow through biochips iseffected by systematic application of pressures to ports located at theends of fluidic channels. When a pressure less than the burst pressureof a capillary valve is applied, fluids will flow along the channel andstop at the capillary valve. Fluids will flow through the valve when apressure greater than the burst pressure of the valve is applied. Apneumatic system is also used to close membrane valves by applying apressure to push a membrane against a valve seat. The sealing pressureof the membrane valve is a function of the applied sealing pressure.Pressures are generated by miniature diaphragm pumps and pressureregulators to provide five discrete pressure levels which are selectedand applied to the output. The system provides eight outputs which areconnected to the manifold through ports on the biochip. The pneumaticsubsystem is computer controlled to achieve the desired flow control.The pneumatic subsystem through systematic application of specificpressure levels to the biochip effects fluid flow to carry out the lysisand PCR within the biochip. FIG. 10 shows an exemplary photograph of abiochip.

Thermal Cycler Subsystem. The thermal cycler comprises a high outputthermoelectric module (IBM) mounted on a high efficiency heat sink andfan assembly (heat pump). A cover clamps down on the biochip to providecompression and efficient thermal transfer between the TEM and thereaction chamber. Thermal losses to the cover are minimized by a layerof insulation between the biochip and cover assembly. Temperaturesensors at surface of the TEM and within a reaction chamber providefeedback to allow rapid ramping to and stability at the desired setpointtemperature. The measured heating and cooling rates at the TEM surfaceare 21.6° C./sec and 21.7° C./sec, and the measured heating and coolingrates of the reaction solution are 14.8° C./sec and 15.4° C./sec.Reaction solutions are heated and cooled 7-fold faster in this thermalcycler compared to that in a fast commercial cycler. Minimal transitiontimes between states allow for rapid and controlled heating and coolingof reaction solutions within the biochip. FIGS. 11 and 12 show exemplaryphotographs of a thermal cycler.

The existing TEM, heatsink, and fan assembly described above has beendesigned to mount directly to the chip chamber and positioned to centerthe PCR chambers on the TEM. The surface of the TEM is positioned tomaximize contact with and minimize stress on the biochip. Thermocouplesensors mounted on the surface of the IBM are accommodated by designingthe biochip to allow mounting pockets for the sensors. Thermal isolationbetween the TEM and the rest of the chip chamber is achieved withthermal breaks to minimize non-uniformity in heating and also maximizethermal response. The compression cover is modified to accommodate theformat of the purification module and biochip and is utilized togenerate the desired pressure for efficient thermal transfer between theTEM and reaction chambers. Thermal isolation between the reactionchamber and cover is accomplished by fabricating an air pocket above thereaction chambers. Ramping and performance of the thermal cycler ischaracterized by placing a thermocouple within the 16 PCR reactionchambers of the biochip.

Separation end Detection Subsystem. The high voltage connections aremounted to the cover of the instrument and make contact to the biochipwhen the cover is closed. The laser induced fluorescence subsystem isintegrated into the instrument with no modification to the optical beampath or subsystem components. The heater subsystem is mounted within thechip chamber.

System status. The thermal cycling subsystem provides the user withdevice status including cycle number, remaining process time, andcurrent block and solution temperatures. User feedback is provided viathe keyboard. All run data is stored on the control computer and alsotransferred by Ethernet to a process database. During separation anddetection on the instrument, the control computer indicates the stepbeing executed. In addition, real-time electropherograms for each of the16 lanes and process parameters including separation channel current andsubstrate temperature are displayed. The onboard computer alerts theuser to the time remaining until annual maintenance, the result ofsystem power-on self test (POST), and the name of any subsystem that hasfailed or requires immediate maintenance.

Example 2

This example demonstrates DNA quantification by microfluidic Picogreenassay using a TH01 locus probe.

An injection molded 16-lane biochip with optically clear reactionchambers was fabricated to allow interrogation of the reaction productswith the optical system described above. Each lane in the biochip holdsapproximately 7 μL reaction mix and allows amplification of 16individual samples simultaneously. PCR conditions were carried out aspreviously described (Giese et al., “Fast Multiplexed PCR forConventional and Microfluidic STR Analysis.” (2009) J. Forensic Sci.Vol. 54, Issue 6, pages 1287-1296). The primer pairs used to target thesingle-copy human tyrosine hydroxylase gene, TH01 (Swango et al.,“Developmental validation of a multiplex qPCR assay for assessing thequantity and quality of nuclear DNA in forensic samples.” (2007)Forensic. Sci. Int. Vol. 170, Issue 1, pages 35-45), were:

TH01 Forward Primer: (SEQ ID NO: 1) 5′ - AGG GTA TCT GGG CTC TGG - 3′TH01 Reverse Primer: (SEQ ID NO: 2)5′ - GCC TGA AAA GCT CCC GAT TAT - 3′Stock 10 ng/μL of 9947A genomic DNA (MCLab, South San Francisco, Calif.)was used to generate a standard curve by adding appropriate quantitiesof DNA in 4 μL volumes to the reaction mix. This standard curvecontained 7 different concentrations of genomic DNA—0 ng, 0.4 ng, 1 ng,4 ng, 10 ng, 20 ng and 40 ng—to use for data fitting of unknown (humanand nonhuman) genomic DNA samples. Standard curve samples were analyzedin quadruplicate. Amplification was initiated with 20 seconds activationat 93° C. followed by 28 cycles of [93° C. for 4 seconds, 58° C. for 15seconds, 70° C. for 7 seconds] and final extension for 90 seconds at 70°C. Completion time was approximately 17 minutes.

Following amplification, Picogreen Reagent® (Invitrogen) was diluted1:200 in TE-4 (10 mM Tris pH 8, 0.01 mm EDTA) buffer and 9 μL of reagentwas is added to 1 lit of PCR product. The resulting solution wasincubated for 5 minutes at room temperature, protected from light. Fromthe 10 μL sample, approximately 6 μL was loaded into a lane of aseparation and detection biochip for instrument laser detection. Theinstrument laser was set to appropriate laser power, gain andintegration time to avoid photobleaching of the dye. The laser was setto output 20 mW and an OD2 neutral density filter (Thorlabs, Newton,N.J.) was used to attenuate the output power to 0.2 mW. The gain of bluePMT was set to 30% of full scale, gain of red, yellow, and green set to0, and the refresh rate set to 5 Hz.

Samples were assayed in quadruplicates. When the laser shutter isopened, the signal will increase to a maximum and then start todecrease. The fluorescence signal strength 1 second (of 5 readings) fromthe maximum signal was recorded. An increase in fluorescence signal wasobserved with increasing input DNA. A plot of input DNA versus relativefluorescence units (RFU) from the instrument has R²=0.999 and was usedas standard curve for extrapolating unknown DNA samples (FIG. 13 ). FIG.14 is the output RFU data from laser detection as a function of lanedisplacement.

Genomic DNAs purified from canine buccal swabs, bacteria (Bacilluscereus), yeast (Saccharomyces cerevisiae), human buccal swabs and humanwhole blood were used to evaluate the assay. Bacterial DNA was extractedfrom bacterial cells or pellets. Canine (Canis familiaris) DNA wasextracted from buccal swabs. Genomic yeast DNA was obtained from ATCC(Manassas, Va.). Fresh human whole blood samples containing EDTA asanticoagulant were obtained on ice from Research Blood Components,L.L.C. (Brighton, Mass.). Human buccal swab samples were obtained bymoving cotton swabs (Bode SecurSwab™) up and down several times on theinside buccal surface of human subjects. Canine buccal swab samples wereobtained similarly. All DNA purifications were performed usingguanidinium-based lysis reagents and purification via silica-DNA bindingspin columns.

Concentrations of these DNA samples were assessed by extrapolating theRFU values from the standard curve generated at the time of theexperiment. DNA concentrations were also measured by UV absorbance usinga Nanodrop spectrophotometer (Thermo Scientific, Wilmington, Del.).Values reported in Table 1 are average values+/−one standard deviation.

TABLE 1 DNA amount (ng) Microfluidic DNA Samples Tested AbsorbancePicogreen Non-human Samples Only Bacillus cereus  9.5 +/− 0.7 Nonedetected Saccharomyces cerevisiae 16 +/− 1 None detected Canisfamiliaris  9.5 +/− 0.7 None detected Non-human Samples Spiked with 10ng Human DNA 10 ng Bacillus cereus + 19.5 +/− 0.7 11 +/− 1 10 ng HumanDNA 16 ng Saccharomyces cerevisiae + 26 +/− 1 11 +/− 2 10 ng Human DNA10 ng Canis familiaris + 19.5 +/− 0.7  6 +/− 1 10 ng Human DNA MockCasework DNA Samples Human Child Buccal Swab DNA 10.2 +/− 0.3 12 +/− 3Human Adult Buccal Swab DNA  9.5 +/− 0.7 12 +/− 2 Human Adult WholeBlood DNA 39 +/− 1 38 +/− 4

Non-human DNA samples generated only background fluorescence signals inthe Picogreen assay but could be detected by UV absorbance. In contrast,known quantities of human genomic DNA spiked with non-human DNAgenerated signals that corresponded to the human DNA contribution.Values obtained from absorbance at 260 nm for human DNA sources wereclose to values from Picogreen curve data fitting. Not only did outputfluorescence signal increase in the presence of higher human genomic DNAtemplate but also, data demonstrated human specificity of the TH01primers.

The advantages of the approach over conventional assays (e.g.,BodeQuant; The Bode Technology Group, Inc., Lorton, Va.) include asubstantial reduction in both sample volume and amplification time. Forexample, amplification following the BodeQuant protocol requires 25 μLof reaction mixture and greater than 60 minutes for a 10-cycle profile.For fluorescence detection, BodeQuant uses a 96-well assay with 200 μLreaction volume per well on a plate reader. Furthermore,platereader-based assays can be quite difficult to integrate in amicrofluidic biochip format. In contrast, the microfluidic assaydescribed here used 7 μL, and the 28-cycle amplification was completedin 17 minutes. The incorporation of the OD2 neutral density opticalfilter reduces laser power by 100-fold, indicating that the number ofamplification cycles and total process time can be reducedsignificantly.

With laser detection and the OD2 optical filter in place, onlyapproximately 0.353 nl of the 10 μl Picogreen reaction solution wasactually excited and detected based on the laser excitation beamdiameter of 30 μm and a 0.5 mm chamber depth. Accordingly, in thisconfiguration, the limit of detection (LOD) of the system is 0.005picogram of DNA. The combination of microfluidic volumes and laserdetection led to a powerful assay. If the OD2 filter is not utilized,the LOD is 0.05 femtograms. Chamber dimensions can be selected to allowan even smaller LOD if desired.

Example 3

This example demonstrates DNA quantification by microfluidic picogreenassay using an Alu locus probe.

The use of a repetitive locus for quantification may allow furtherreduction in reaction time and improvement in LOD. Human Alu sequencesare repetitive elements that are present in hundreds of thousands ofcopies in the genome, and a primer pair targeting Alu sequences was usedfor microfluidic quantification:

Alu Forward Primer: (SEQ ID NO: 3)5′ - GTC AGG AGA TCG AGA CCA TCC C- 3′ Alu Reverse Primer:(SEQ ID NO: 4) 5′ - TCC TGC CTC AGC CTC CCA AG - 3′Fast PCR cycling profile reactions and quantification were as describedin Example 2 with a modified amplification protocol of 20 secondsactivation at 93° C. followed by 15-cycles of [93° C. for 4 seconds, 58°C. for 15 seconds, 70° C. for 7 seconds] and final extension for 90seconds at 70° C. Completion time was approximately 10 minutes. A plotof input DNA versus relative fluorescence units (RFU) from theinstrument has R²=0.999 (FIG. 15 ). FIG. 16 is the output RFU data fromlaser detection as a function of lane displacement. During excitation, afilter that decreased the laser power strength by a magnitude comparedto that used with TH01 reaction was found necessary to avoidphotobleaching of the dye. An OD4 neutral density optical filter wasused with laser power set to 200 mW, gain of blue PMT to 30% of fullscale, gain of red, yellow, and green set to 0, and refresh rate at 5Hz. At this laser power setting and filter combination, the effectivelaser power is 10% that of Example 2. This data suggests that cyclenumber during amplification can be further reduced.

To test this possibility, 15 samples were quantified each with input DNAof 1, 5, 10, and 30 ng using 10 amplification cycles, reducingamplification time by 2.5 minutes. The signal strength increases withincreasing input DNA (FIG. 17 ). For 1 ng of input, the baselinesubtracted signal strength is 19.9 RFU with a standard deviation of 10RFU and a CV of 50%. For 5 ng of input, the baseline subtracted signalstrength is 68 RFU with a standard deviation of 11 RFU and a CV of 17%.

Human genomic DNA, non-human DNA, and spiked human genomic were used toevaluate the assay as in Example 2. Cattle (Bos taurus) and chicken(Gallus domesticus) were extracted from blood samples. All DNAs wereprepared as in Example 2.

TABLE 2 DNA amount (ng) Microfluidic DNA Samples Tested AbsorbancePicogreen Non-human Samples Only Bacillus subtilis 10 +/− 0 Nonedetected Bacillus cereus  9.9 +/− 0.1 None detected Bacillus megaterium 9.8 +/− 0.3 None detected Saccharomyces cerevisiae 20.5 +/− 0.7 Nonedetected Canis familiaris  9.5 +/− 0.7 None detected Bos taurus 10 +/− 00.5 +/− 0.1 Gallus domesticus 10 +/− 0 1.4 +/− 1.1 Non-human SamplesSpiked with 10 ng Human DNA 10 ng Bacillus subtilis + 20 +/− 0 5.1 +/−0.7 10 ng Human DNA 10 ng Bacillus cereus + 19.9 +/− 0.1 5.5 +/− 0.5 10ng Human DNA 10 ng Bacillus megaterium + 19.8 +/− 0.3 5.5 +/− 0.8 10 ngHuman DNA 20 ng Saccharomyces cerevisiae + 30.5 +/− 0.7 8 +/− 1 10 ngHuman DNA 10 ng Canis familiaris + 19.5 +/− 0.7 9.9 +/− 0.6 10 ng HumanDNA 10 ng Bos taurus + 10 ng Human DNA 20 +/− 0 11.5 +/− 0.3  10 ngGallus domesticus + 20 +/− 0 11.3 +/− 2.5  10 ng Human DNAMock forensic casework samples were also used for evaluation. Wet bloodsamples on swabs were prepared by pipetting 100 μL of blood suspensiononto a ceramic tile and then collecting the blood with cotton swabs.Dried blood samples were prepared similarly but allowed to dryovernight. Cellular samples were collected by rubbing the swab head(pre-wet with sterile water), on the palm of a human subject. Touchsamples were prepared by using a pre-wet swab on a ceramic tile that washandled several times by a single donor. All DNA extractions wereperformed using the QIAmp Kit (Qiagen, Valencia, Calif.) following themanufacturer's protocol for isolation of genomic DNA from swabs.

TABLE 3 DNA amount (ng) Microfluidic DNA Samples Tested AbsorbancePicogreen 10 ng Non-human Samples Only Dry Human Whole Blood DNA 18.9+/− 2.6 22.0 +/− 0.1  Wet Human Whole Blood Swab DNA 11.5 +/− 0.7 14.6+/− 1.2  Wet Human Whole Blood 19.5 +/− 1.0 15.1 +/− 0.3  Suspension DNAHuman Cellular Swab DNA  3.9 +/− 0.1 5.9 +/− 0.5 Human Touch Swab DNA 8.3 +/− 1.0 9.0 +/− 0.1 Human Adult Buccal Swab DNA  9.5 +/− 0.7 9.8+/− 2.8 Human Baby Buccal Swab DNA 10.2 +/− 0.3 8.3 +/− 2.2Based on these data, it is clear that the microfluidic Alu Picogreenassay is highly sensitive and specific for human genomic DNAquantification. Alu amplification has the benefit of approximately onemillion-fold greater target than the TH01 amplification; thus, ifamplification is 100% efficient, represents a requirement ofapproximately 8 amplification cycles as opposed to 28. The 10-foldreduced laser power in the Alu case represents approximately 3additional required cycles. In theory, under these conditions, the Alureaction should require 11 cycles to generate a signal comparable to the28-cycle TH01 reaction. Although amplification of the two loci isunlikely to be identical, the observed results at 10 cycles closelymatch these theoretical considerations.

Using Alu probes, the combination of microfluidic volumes and laserdetection leads to an LOD of 0.005 picograms of DNA. Without placementof an OD3-equivalent laser filter, the resulting LOD is 0.005femtograms. This LOD is an order of magnitude better than the use ofTH01 probes and the amplification and detection conditions of Example 2;the Alu probes and condition also allow a significant reduction in cyclenumber. In some embodiments, if LODs of less than 0.005 femtograms arerequired, one or more of the number of amplification cycles, thesequence and efficiency of the probe, and laser power can be increased.

Example 4

This example demonstrates DNA quantification by SYBR Green I assay.

The amplification reaction components including Alu primers described inExample 3 were used, with the exception that a 1:60,000 dilution of SYBRGreen I (Invitrogen) in Tris EDTA Buffer (pH 8) was incorporated intothe PCR mix. SYBR Green I is a thermally stable fluorescent dye and cantherefore be added into the PCR mix as in real-time PCR assays.

To test workability of this faster assay, standard calibration curveswere generated and reproduced. Genomic 9947A DNA standards were: 0 ng,0.4 ng, 1 ng, 4 ng, 10 ng, 20 ng and 30 ng Amplification was initiatedwith 20 seconds activation at 93° C. followed by 7-cycles of [93° C. for4 seconds, 58° C. for 15 seconds, 70° C. for 7 seconds] and finalextension for 90 seconds at 70° C. Completion time was 6 minutes.Following amplification, the same biochip was subjected to laserexcitation with optical settings as in Example 3. PCR in biochip andlane detection were performed in quadruplicate to confirmreproducibility of the standard curve and that fluorescence increaseswith increase in input template DNA. A plot of input DNA versus RFU fromfrom the instrument (FIG. 18 ) gave a polynomial fit with R²=0.995. Theadvantage of this approach over the use of Picogreen dye is thatamplification and detection can be performed in the identical chambersof the biochip, simplifying the overall process (e.g. eliminating theneed to meter the Picogreen reagent and mix it with thepost-amplification reaction) and biochip format.

Example 5

This example demonstrates DNA quantification without prior amplificationby hybridization assay using molecular beacons.

Direct hybridization without amplification was utilized to quantifyhuman genomic DNA. Two beacon probes were designed such that they targetthe repetitive human Alu elements. Probe 1 was derived from PV 92 geneand has the sequence 5′-GCC CGA TTT TGC GAC TTT GGA GGG C-3′ (SEQ ID NO:5) (Human Alu Repeat GenBank Accession Numbers: M57427.1/M33776,AF302689). Probe 2 was designed by alignment of known Alu-subfamiliesand choosing a target region that was highly conserved. The sequence5′-CGC CTC AAA GTG CTG GGA TTA CAG GCG-3′ (SEQ ID NO: 6) was predictedto be a more sensitive probe. Both probes have fluorescein (6 FAM™)attached at the 5′ end and Iowa Black Quencher (IB®FQ) attached at the3′ end (Integrated DNA Technologies [IDT], Coralville, Iowa).

The fluorescence buffer appropriate for Probe 1 contained: 40 mM NaCl, 5mM MgCl₂ and 10 mM Tris-HCl (pH 8.0). The fluorescence bufferappropriate for Probe 2 contained: 1 mM MgCl₂ and 20 mM Tris-HCl (pH8.0). The fluorescence buffers were chosen based on hybridization withan artificial ssDNA target which gave high signal-to-noise ratios.Melting temperatures (T_(m)) of the hybrid and the stem structure weredetermined using IDT SciTools OligoAnalyzer 3.1 and mfold version 3.4programs. The hybridization temperature was set to 53° C., a temperaturebelow the T_(m) of the hybrid and slightly higher than the T_(m) of thestem.

22 μL sample reactions in desired fluorescence buffer were prepared with2 μL of 10 μM molecular beacon and varying concentrations of humangenomic DNA (0, 4.5, 9, 18, 32, 50 and 100 ng/μL) (Roche AppliedScience, Indianapolis, Ind.). Approximately 7 μL was then transferredinto the biochip of Examples 2-4 for thermal denaturation andhybridization. The thermal profile for the biochip was initiated with asingle cycle of 10 seconds denaturation at 95° C. followed byhybridization for 60 seconds at 53° C. and cool down for 60 seconds at25° C. The biochip was then subsequently analyzed in from theinstrument. When probe 1 was utilized, laser power was set to 20 mW,gain of blue PMT to 30% of full scale with all the rest of the colorsset to 0 and refresh rate at 10 Hz. For probe 2, however, use of an OD2neutral density optical filter was necessary and the rest of thesettings were implemented as in probe 1. This confirmed the increasedsensitivity of probe 2 over probe 1. Samples were assessed inquadruplicates, and a set of control samples was prepared similarly butwithout human genomic DNA.

FIG. 19 is the hybridization plot of RFU versus input DNA detected usingmolecular beacon probe 1. The average RFU signal for the negativecontrol is 3427 RFU with SD of 216 RFU and for the 4.5 ng/μL total inputwas 4641 RFU with SD of 583 RFU. FIG. 20 is the hybridization plot usingmolecular beacon probe 2. The average RFU signal for the negativecontrol was 3668 RFU with SD of 33 RFU and for the 4.5 ng/μL total inputwas 4075 RFU with SD of 83 RFU. Baseline subtracted RFUs were plottedagainst actual input DNA detected by laser. This translated the totalhuman genomic DNA of 0, 4.5, 9, 18, 32, 50 and 100 ng/μL to 0, 1.6, 3.2,6.4, 11.3, 17.6 and 35.3 picograms of DNA, respectively. Increase insignal due to hybrid formation increased with increasing target DNApresent in the sample. The data demonstrated that the two probesconsistently distinguished between 0 and 1.6 picograms of DNA. The LODusing probe 1 was 1.6 picograms. For probe 2, without the OD2 laserfilter, the assay can detect approximately 16 femtograms of DNA. Notethat this LOD is almost three orders of magnitude less than the DNApresent in a single human cell (approximately 6 picograms) and allowseffective quantification of trace forensic evidence.

As those skilled in the art will appreciate, modifications to the Alubeacons (e.g., using more highly conserved target sequences and coupledfluorophores with better quenching efficiency) can further improve thesensitivity and LOD of the direct hybridization approach. However, interms of the Alu probes used in this example, direct hybridization hasabout the same sensitivity as that of the 10-cycle PCR-Picogreen assay.However, with respect to the process time, hybridization withoutamplification assay required only approximately two minutes, shorteningthe overall quantification by approximately 5 minutes. In addition, thedirect hybridization offers a significant overall cost-reduction andsimplifies the integrated microfluidic system since enzymes, dNTPs andPCR buffers which require real estate on the microfluidic biochip arenot involved in the reaction. Finally, PCR inhibitors commonly presentin clinical, environmental, and forensic samples should not inhibit thehybridization reaction.

Example 6

This example demonstrates reducing reaction time of the directhybridization molecular beacon assay.

Reaction conditions for molecular beacon probe 2 were carried outsimilarly to those of Example 5 but with a single cycle of 10 secondsdenaturation at 95° C. followed by hybridization for 30 seconds at 53°C. and final cool down for 10 seconds at 25° C. The same opticalsettings were also implemented. FIG. 21 is the hybridization plot of RFUversus input DNA translated to actual picograms DNA quantified anddetected. The average RFU signal for the negative control is 3321 RFUwith SD of 105 RFU and for 1.6 picograms is 3806 RFU with SD of 61 RFU.The data suggests that reducing the overall quantification time from to130 seconds to 50 seconds had no effect on the assay. In fact, furtheroptimization (with and without an improved probe) will allow assay timeto be reduced to less than 15 seconds (e.g. denaturation of 3 seconds,hybridization of 10 seconds, and cool down of 1 second).

Example 7

This example demonstrates direct hybridization molecular beacon assay toquantify human buccal swab DNA.

From the standard curve of Example 6, fluorescence signals of buccalswab DNAs from male and female human subjects were extrapolated andcompared with values obtained from UV absorbance.

TABLE 4 DNA amount (pg) DNA Samples Tested Absorbance Beacon Assay HumanAdult Male 105.3 +/− 0.1 112.4 +/− 22.7 Buccal Swab DNA Human AdultFemale 152.2 +/− 0.6 152.2 +/− 53.7 Buccal Swab DNA

Example 8

This example demonstrates specificity of the direct hybridizationmolecular beacon assay. Non-human DNAs were purified as described. Fromthe standard curve of Example 6, fluorescence signals from bacteria,canine, and chicken DNAs were again extrapolated and compared withvalues obtained from UV absorbance. In addition, a known human buccalswab DNA sample was spiked with these different background DNAs.

TABLE 5 DNA amount (pg) DNA Samples Tested Absorbance Beacon AssayNon-human Samples Only Bacillus cereus 436.4 +/− 3.5  38.6 +/− 32.4Saccharomyces cerevisiae 327.3 +/− 3.2 74.8 +/− 1.1 Canis familiaris210.4 +/− 0.6  84.4 +/− 13.7 Gallus domesticus 234.9 +/− 1.4  73.1 +/−36.9 Human DNA Spiked Samples 436.4 pg Bacillus cereus + 542 119.3 +/−2.0  105.3 pg Human DNA 210.4 pg Canis familiaris + 316 101.2 +/− 24.5105.3 pg Human DNA 234.9 pg Gallus domesticus + 340 105.2 +/− 12.0 105.3pg Human DNAAlthough non-human DNAs from the beacon assay gave fluorescence signalsslightly above background, this artifact is likely due to buffereffects. Background DNA samples used in the assay were resuspended in TEbuffer and not in fluorescence buffer. It was noted previously thatbeacons buffer components can contribute to the detected fluorescence.Fast direct hybridization allows human-specific DNA quantification inheterogeneous samples.

Example 9

This example demonstrates eliminating the need for quantification withforensic database samples.

The amount of DNA collected by buccal swabbing is highly variable andranges from approximately 100 ng to greater than 10 μg, although themajority of samples contain between 500 ng and 4 μg of DNA. In thelaboratory, this variability has minimal impact on the overall STRtyping process as purified DNA is subjected to quantification, and adesired amount of DNA is utilized in the subsequent PCR reaction.

Buccal swab DNA was purified using a guanidinium-based silica bindingapproach modified from that described in U.S. patent application Ser.No. 12/699,564, entitled “Nucleic Acid Purification,” filed Feb. 3,2010, by Selden et al., which is incorporated herein by reference.Buccal cell samples from 15 human subjects were obtained as described inExample 3. The swab's shaft was cut at score line to fit into a 2 mLmicrocentrifuge tube. A master mix of lysis buffer containingguanidinium hydrochloride and detergent solution, and proteinase K(Qiagen, Valencia, Calif.) was prepared. 500 μL of this lysis solutioncontaining 0.5 mg of proteinase K was transferred into each of thetubes. The solution was thoroughly mixed by vortexing for 5 seconds. 550μL absolute ethanol was added to the mixture and again vortexed for 5seconds. 100 μL of the homogenized flow-through was manually loaded intothe biochip's input port. This biochip has a 1.5 mm DNA-binding silicamembrane for purification. The binding membrane was washed with 2 mL ofethanol-isopropanol-NaCl wash solution. Prior to elution, the bindingmembrane was allowed to dry for 30 seconds. DNA was eluted with 600 μLof TE-4 (10 mM Tris-HCl, pH 8 and 0.1 mM EDTA).

Following generation of reference sample DNA, 7 μL PCR reaction mixescontained 3.4 μL of the biochip-purified DNA and 1× Powerplex16 primers(Promega Corporation, Madison, Wis.) were prepared. Note that noquantification step was performed prior to amplification—a fixed volumeof the purified DNA was always used for the amplification reaction. As acontrol, a standard 1 ng 9947A genomic DNA diluted from stock in TE-4was also amplified. Amplification started with 20 seconds activation at93° C. followed by 30 cycles of [93° C. for 4 seconds, 56° C. for 20seconds, 70° C. for 20 seconds] and final extension for 90 seconds at70° C. Completion time was approximately 25 minutes.

DNA samples for analysis from the instrument were prepared by manuallypipetting the samples into the sample reservoirs of the separationbiochip. In particular, 2.7 μL of the amplified product, 0.3 μL of HD400sizing standard, and 10 μL of HiDi were mixed together and loaded intothe sample wells. After loading the samples and buffers, the biochip wasplaced into the instrument with electric fields applied to separate anddetect the amplified DNA. Instrument and detections were performed induplicate for each buccal swab DNA sample amplified. Peak heights ofhomozygous alleles at a given locus were divided by 2 to allowcomparisons with peak heights of heterozygous alleles at thecorresponding locus. Average peak heights of all loci from the 1 nginput 9947A control DNA were used to estimate the quantity of input DNAinto the PCR reactions. Based on this signal strength analysis, thequantity of DNA from the 15 buccal swab extracts were all within the1.26-2.50 ng, and most samples contained between 1.5 and 2.25 ng per 3.4μL into PCR.

TABLE 6 Sample [PCR Input DNA] (ng/μL) 1 0.71 2 0.61 3 0.64 4 0.61 50.52 6 0.54 7 0.54 8 0.58 9 0.64 10 0.41 11 0.49 12 0.56 13 0.47 14 0.4615 0.47 Control 9947 A 0.29The variable recovery in swab purification and the enormous excess ofrecovered DNA have been addressed by controlling the binding capacity ofthe binding membrane. FIG. 22 demonstrates this “cut-off” approach. DNAbinding capacity scales with the number of layers of a 7 mm silicamembrane used for DNA binding. Similarly, the binding capacity of thebinding membrane also scales with the active diameter of the bindingmembrane. FIG. 23 shows the binding performance of a 1 mm diameterbinding membrane over a range of DNA inputs. The DNA yield increaseslinearly with DNA input level for input levels below 600 ng, and theyield saturates at approximately 300 ng of DNA for inputs of 600 ng ormore. In a setting in which microfluidic DNA purification is integratedwith amplification (or other processing steps as desired), knowledge ofthe range of recovered DNA allows significant flexibility in biochipdesign. In the processing of forensic reference samples, a fraction ofthe lysate may be subjected to purification (note that the 1.26-2.50 ngof DNA used for PCR translates to 220-440 ng of DNA in the 600 μLelution volume as only a tenth of the lysate material was purified). Byreducing the quantity of DNA to be purified, the binding capacity of thepurification media can be reduced concomitantly. The ability to generatepurified nucleic acids within a predetermined, defined range withoutquantification can simplify biochip design, further reduce cost, andfurther accelerate process timing.

Example 10

This example demonstrates development of excitation and detectionparameters for quantification based on a specific optical train.

A master mix of DNA and Picogreen intercalating dye was prepared andinserted into the quantification biochip and used for excitation anddetection with the quantification instrument. Under laser excitation,detector signal strength increased with increasing PMT gain. Signalstrength increased over 3 orders of magnitude, from 10 RFU and 10,600,as the PMT gains were swept across their operation range (FIG. 24 ). Thesignal to noise ratio increased with increasing PMT gain, up to asetting of 30%, and saturates at approximately 22 for PMT gains of 30%and higher. This data set shows that a PMT gain setting of 30% noisecontribution associated with the detection electronics was negligible.The gain setpoint of 30% was optimal for use to maximizesignal-to-noise, signal strength, and dynamic range (FIG. 25 ).

The effect of laser excitation on signal strength is shown in FIG. 26 .The two datasets were generated using neutral density optical filters,with optical densities of 4 and 2, to reduce the excitation power at thesample by 10000 and 100 times that of the laser output. The data showssignal strength increasing with excitation power for both datasets. Amoderate excitation power (0.02 mW) incident on the sample generated arelatively constant signal strength over time. This signal strength wasconsistent with the concentration of fluorophores in the sample. A highlevel of excitation (2 mW) incident on the sample exhibit an exponentialdecay to a level that was independent of the number of fluorophores inthe sample. The high level of excitation incident on the sample resultedin photochemical destruction of a fluorophore, also known asphotobleaching, and an irreversible loss of fluorescence activity in thesample (FIG. 27 ). These results show that a sample excitation power of0.2 mW was optimal for quantification. Taken together, the results showthat a PMT gain of 30% and an excitation power of 0.2 mW are setpointsto achieve optimal signal-to-noise, sensitivity, dynamic range with theexcitation and detection instrument.

While several embodiments of the present invention have been describedand illustrated herein, those of ordinary skill in the art will readilyenvision a variety of other means and/or structures for performing thefunctions and/or obtaining the results and/or one or more of theadvantages described herein, and each of such variations and/ormodifications is deemed to be within the scope of the present invention.More generally, those skilled in the art will readily appreciate thatall parameters, dimensions, materials, and configurations describedherein are meant to be exemplary and that the actual parameters,dimensions, materials, and/or configurations will depend upon thespecific application or applications for which the teachings of thepresent invention is/are used. Those skilled in the art will recognize,or be able to ascertain using no more than routine experimentation, manyequivalents to the specific embodiments of the invention describedherein. It is, therefore, to be understood that the foregoingembodiments are presented by way of example only and that, within thescope of the appended claims and equivalents thereto, the invention maybe practiced otherwise than as specifically described and claimed. Thepresent invention is directed to each individual feature, system,article, material, kit, and/or method described herein. In addition, anycombination of two or more such features, systems, articles, materials,kits, and/or methods, if such features, systems, articles, materials,kits, and/or methods are not mutually inconsistent, is included withinthe scope of the present invention.

All definitions, as defined and used herein, should be understood tocontrol over dictionary definitions, definitions in documentsincorporated by reference, and/or ordinary meanings of the definedterms.

The indefinite articles “a” and “an,” as used herein in thespecification and in the claims, unless clearly indicated to thecontrary, should be understood to mean “at least one.”

The phrase “and/or,” as used herein in the specification and in theclaims, should be understood to mean “either or both” of the elements soconjoined, i.e., elements that are conjunctively present in some casesand disjunctively present in other cases. Multiple elements listed with“and/or” should be construed in the same fashion, i.e., “one or more” ofthe elements so conjoined. Other elements may optionally be presentother than the elements specifically identified by the “and/or” clause,whether related or unrelated to those elements specifically identified.Thus, as a non-limiting example, a reference to “A and/or B”, when usedin conjunction with open-ended language such as “comprising” can refer,in one embodiment, to A only (optionally including elements other thanB); in another embodiment, to B only (optionally including elementsother than A); in yet another embodiment, to both A and B (optionallyincluding other elements); etc.

As used herein in the specification and in the claims, “or” should beunderstood to have the same meaning as “and/or” as defined above. Forexample, when separating items in a list, “or” or “and/or” shall beinterpreted as being inclusive, i.e., the inclusion of at least one, butalso including more than one, of a number or list of elements, and,optionally, additional unlisted items. Only terms clearly indicated tothe contrary, such as “only one of” or “exactly one of,” or, when usedin the claims, “consisting of,” will refer to the inclusion of exactlyone element of a number or list of elements. In general, the term “or”as used herein shall only be interpreted as indicating exclusivealternatives (i.e. “one or the other but not both”) when preceded byterms of exclusivity, such as “either,” “one of,” “only one of,” or“exactly one of.” “Consisting essentially of,” when used in the claims,shall have its ordinary meaning as used in the field of patent law.

As used herein in the specification and in the claims, the phrase “atleast one,” in reference to a list of one or more elements, should beunderstood to mean at least one element selected from any one or more ofthe elements in the list of elements, but not necessarily including atleast one of each and every element specifically listed within the listof elements and not excluding any combinations of elements in the listof elements. This definition also allows that elements may optionally bepresent other than the elements specifically identified within the listof elements to which the phrase “at least one” refers, whether relatedor unrelated to those elements specifically identified. Thus, as anon-limiting example, “at least one of A and B” (or, equivalently, “atleast one of A or B,” or, equivalently “at least one of A and/or B”) canrefer, in one embodiment, to at least one, optionally including morethan one, A, with no B present (and optionally including elements otherthan B); in another embodiment, to at least one, optionally includingmore than one, B, with no A present (and optionally including elementsother than A); in yet another embodiment, to at least one, optionallyincluding more than one, A, and at least one, optionally including morethan one, B (and optionally including other elements); etc.

It should also be understood that, unless clearly indicated to thecontrary, in any methods claimed herein that include more than one stepor act, the order of the steps or acts of the method is not necessarilylimited to the order in which the steps or acts of the method arerecited.

In the claims, as well as in the specification above, all transitionalphrases such as “comprising,” “including,” “carrying,” “having,”“containing,” “involving,” “holding,” “composed of,” and the like are tobe understood to be open-ended, i.e., to mean including but not limitedto. Only the transitional phrases “consisting of” and “consistingessentially of” shall be closed or semi-closed transitional phrases,respectively, as set forth in the United States Patent Office Manual ofPatent Examining Procedures, Section 2111.03.

What is claimed is: 1-183. (canceled)
 184. An instrument for excitationand detection of fluorophores in a plurality of functional regions in abiochip, comprising: an excitation source; and a steering element thatdirects a beam from an excitation source to a plurality of functionalregions in the biochip, wherein the excitation source excites thefluorophores in the plurality of functional regions generating a signalthat is detected such that said signal from at least one of theplurality of functional regions allows nucleic acid quantification. 185.The instrument of claim 184 wherein the steering element is a mirror.186. The instrument of claim 184, further comprising a first scannerthat directs the excitation beam to each of the quantification chambersin the quantification region of the biochip and a second scanner thatdirects the excitation beam to each of the chambers in a secondfunctional region of the biochip.
 187. The instrument of claim 184,further comprising a mirror mounted on a translation stage that directsthe excitation beam to each of the quantification chambers in thequantification region of the biochip and a second scanner that directsthe excitation beam to each of the chambers in a second functionalregion of the biochip.
 188. The system of claim 184 wherein said firstfunctional region on said biochip is a quantification region and asecond functional region is an amplification region, a fragmentseparation and detection region, a nucleic acid sequencing region, anultrafiltration region or a mixing region.
 189. The system of claim 184wherein the second functional region of said biochip is a separation anddetection region.